Revision as of 17:46, 9 January 2017 by >Shicheng
Background
- Epigenomic analysis detects aberrant super-enhancer DNA methylation in human cancer
- https://www.ncbi.nlm.nih.gov/pubmed/26497311
- WGBS by 101 bp pair-end sequencing.
- Phred Score: 33
- 11 primary tumor tissue, 2 metastasis tissue and 9 normal tissues
Method and Procedure
Sample
File
|
title
|
geo_accession
|
status
|
organism_ch1
|
treatment_protocol_ch1
|
description.1
|
data_processing
|
GSM1279516_CpGcontext.Brain_W.txt.gz |
GSM1279516 |
Brain_white matter |
GSM1279516 |
Normal |
sample type: Primary |
Brain_WNT |
SRX381706
|
GSM1279517_CpGcontext.Breast.txt.gz |
GSM1279517 |
Breast_normal |
GSM1279517 |
Normal |
sample type: Primary |
Breast_NT |
SRX381631
|
GSM1279518_CpGcontext.CD19.txt.gz |
GSM1279518 |
Blood_B-cells_CD19 |
GSM1279518 |
Normal |
sample type: Primary |
CD19_NT |
SRX381725
|
GSM1279519_CpGcontext.Colon.txt.gz |
GSM1279519 |
Colon_normal |
GSM1279519 |
Normal |
sample type: Primary |
Colon_NT |
SRX381553
|
GSM1279520_CpGcontext.Colon_M.txt.gz |
GSM1279520 |
Colon_metastasis |
GSM1279520 |
Metastasis |
sample type: Primary |
Colon_MC |
SRX381585
|
GSM1279521_CpGcontext.Colon_P.txt.gz |
GSM1279521 |
Colon_cancer |
GSM1279521 |
Cancer |
sample type: Primary |
Colon_PC |
SRX381569
|
GSM1279522_CpGcontext.H1437.txt.gz |
GSM1279522 |
Lung_H1437 |
GSM1279522 |
Adenocarcinoma |
sample type: Cell line |
H1437_LCC |
SRX381716
|
GSM1279523_CpGcontext.H157.txt.gz |
GSM1279523 |
Lung_H157 |
GSM1279523 |
Squamous cell cancer |
sample type: Cell line |
H157_LCC |
SRX381719
|
GSM1279524_CpGcontext.H1672.txt.gz |
GSM1279524 |
Lung_H1672 |
GSM1279524 |
Small cell lung cancer |
sample type: Cell line |
H1672_LCC |
SRX381722
|
GSM1279527_CpGcontext.Lung.txt.gz |
GSM1279527 |
Lung_normali |
GSM1279527 |
Normal |
sample type: Primary |
Lung_NT |
SRX381713
|
GSM1279532_CpGcontext.U87MG.txt.gz |
GSM1279532 |
Brain_U87MG |
GSM1279532 |
Glioma |
sample type: Cell line |
U87MG_BC |
SRX381701`
|
SRA Download
SRA to Fastq
wget -r -nd ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA112/SRA112056/SRX381553
wget -r -nd ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA112/SRA112056/SRX381569
wget -r -nd ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA112/SRA112056/SRX381585
wget -r -nd ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA112/SRA112056/SRX381601
wget -r -nd ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA112/SRA112056/SRX381611
wget -r -nd ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA112/SRA112056/SRX381621
wget -r -nd ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA112/SRA112056/SRX381631
wget -r -nd ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA112/SRA112056/SRX381646
wget -r -nd ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA112/SRA112056/SRX381661
wget -r -nd ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA112/SRA112056/SRX381666
wget -r -nd ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA112/SRA112056/SRX381671
wget -r -nd ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA112/SRA112056/SRX381678
wget -r -nd ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA112/SRA112056/SRX381693
wget -r -nd ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA112/SRA112056/SRX381697
wget -r -nd ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA112/SRA112056/SRX381701
wget -r -nd ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA112/SRA112056/SRX381706
wget -r -nd ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA112/SRA112056/SRX381710
wget -r -nd ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA112/SRA112056/SRX381713
wget -r -nd ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA112/SRA112056/SRX381716
wget -r -nd ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA112/SRA112056/SRX381719
wget -r -nd ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA112/SRA112056/SRX381722
wget -r -nd ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA112/SRA112056/SRX381725
trim_glore
Fastq to Bam
Sample
|
N(reads)
|
N(mapped)
|
P(mapping)
|
N(C)
|
N(MCPG)
|
N(MCHG)
|
N(MCHH)
|
N(UCPG)
|
N(UCHG)
|
N(UCHH)
|
P(MCPG)
|
P(MCHG)
|
P(MCHH)
|
SRR1035722_1 |
36231449 |
26356409 |
72.7% |
992806465 |
56929401 |
665378 |
1462755 |
24444494 |
281230022 |
628074415 |
70.0% |
0.2% |
0.2%
|
SRR1035723_1 |
38672444 |
28821090 |
74.5% |
1093399553 |
63203116 |
573053 |
1246437 |
27172725 |
309871245 |
691332977 |
69.9% |
0.2% |
0.2%
|
SRR1035724_1 |
38169545 |
28474993 |
74.6% |
1078721744 |
62354261 |
576320 |
1254164 |
26757183 |
305665500 |
682114316 |
70.0% |
0.2% |
0.2%
|
SRR1035725_1 |
35676108 |
26566972 |
74.5% |
1019460690 |
60060766 |
502315 |
1114013 |
26113507 |
289896735 |
641773354 |
69.7% |
0.2% |
0.2%
|
SRR1035726_1 |
42115048 |
31984957 |
75.9% |
1213271012 |
70615619 |
707726 |
1468673 |
29983057 |
343628632 |
766867305 |
70.2% |
0.2% |
0.2%
|
SRR1035727_1 |
42756295 |
32415649 |
75.8% |
1227727881 |
71552761 |
716711 |
1484636 |
30188318 |
347670963 |
776114492 |
70.3% |
0.2% |
0.2%
|
SRR1035728_1 |
42411383 |
32186391 |
75.9% |
1220313570 |
71002070 |
724203 |
1493462 |
30218679 |
345662242 |
771212914 |
70.1% |
0.2% |
0.2%
|
SRR1035729_1 |
42623243 |
32307805 |
75.8% |
1223735711 |
71070930 |
718040 |
1481741 |
30319685 |
346663966 |
773481349 |
70.1% |
0.2% |
0.2%
|
SRR1035730_1 |
42047512 |
31854981 |
75.8% |
1206042893 |
70201432 |
742769 |
1511214 |
29815343 |
341471569 |
762300566 |
70.2% |
0.2% |
0.2%
|
SRR1035731_1 |
42403142 |
32112901 |
75.7% |
1215614793 |
70706477 |
725488 |
1482816 |
30013259 |
344211647 |
768475106 |
70.2% |
0.2% |
0.2%
|
SRR1035732_1 |
33362690 |
24707272 |
74.1% |
941095281 |
55251654 |
457269 |
1019789 |
23501401 |
267177061 |
593688107 |
70.2% |
0.2% |
0.2%
|
SRR1035733_1 |
33381741 |
24709065 |
74.0% |
941288700 |
55277191 |
455919 |
1016786 |
23547047 |
267294566 |
593697191 |
70.1% |
0.2% |
0.2%
|
SRR1035734_1 |
33196884 |
24571704 |
74.0% |
936212940 |
54864931 |
451643 |
1005279 |
23520896 |
265896154 |
590474037 |
70.0% |
0.2% |
0.2%
|
SRR1035735_1 |
33985218 |
25130974 |
73.9% |
956402792 |
55943101 |
474478 |
1057439 |
24011066 |
271578107 |
603338601 |
70.0% |
0.2% |
0.2%
|
SRR1035736_1 |
33887645 |
25047606 |
73.9% |
952060048 |
55686131 |
457557 |
1021131 |
23788426 |
270227147 |
600879656 |
70.1% |
0.2% |
0.2%
|
SRR1035737_1 |
33354700 |
24650161 |
73.9% |
936151932 |
54670947 |
455043 |
1013284 |
23463753 |
265750296 |
590798609 |
70.0% |
0.2% |
0.2%
|
SRR1035738_1 |
40126453 |
31958454 |
79.6% |
1170141034 |
54984718 |
720678 |
1774947 |
27387084 |
313488867 |
771784740 |
66.8% |
0.2% |
0.2%
|
SRR1035739_1 |
42630446 |
34724930 |
81.5% |
1280677712 |
60798490 |
611014 |
1482864 |
30244382 |
343441526 |
844099436 |
66.8% |
0.2% |
0.2%
|
SRR1035740_1 |
42154379 |
34384348 |
81.6% |
1266363559 |
60128458 |
613867 |
1500954 |
29880923 |
339603738 |
834635619 |
66.8% |
0.2% |
0.2%
|
SRR1035741_1 |
39992910 |
32461489 |
81.2% |
1211429605 |
58662506 |
543038 |
1348799 |
29379031 |
326181180 |
795315051 |
66.6% |
0.2% |
0.2%
|
SRR1035742_1 |
46418632 |
38547447 |
83.0% |
1420008578 |
67810264 |
759476 |
1759239 |
33343955 |
380559074 |
935776570 |
67.0% |
0.2% |
0.2%
|
SRR1035743_1 |
47276691 |
39199235 |
82.9% |
1441569094 |
68899681 |
769964 |
1782273 |
33700891 |
386228454 |
950187831 |
67.2% |
0.2% |
0.2%
|
SRR1035744_1 |
46542012 |
38617083 |
83.0% |
1421723100 |
67864941 |
776755 |
1779701 |
33458732 |
381130422 |
936712549 |
67.0% |
0.2% |
0.2%
|
SRR1035745_1 |
46843070 |
38812333 |
82.9% |
1427699210 |
68060537 |
765033 |
1764230 |
33641134 |
382643861 |
940824415 |
66.9% |
0.2% |
0.2%
|
SRR1035746_1 |
46170806 |
38253135 |
82.9% |
1406415812 |
67159539 |
796772 |
1804119 |
33062801 |
376849829 |
926742752 |
67.0% |
0.2% |
0.2%
|
SRR1035747_1 |
46544502 |
38538932 |
82.8% |
1416472851 |
67597445 |
776087 |
1766890 |
33272512 |
379517129 |
933542788 |
67.0% |
0.2% |
0.2%
|
SRR1035748_1 |
36600721 |
29621066 |
80.9% |
1096324957 |
52954395 |
483095 |
1207263 |
25998029 |
294582645 |
721099530 |
67.1% |
0.2% |
0.2%
|
SRR1035749_1 |
36640873 |
29622158 |
80.8% |
1096474862 |
53014044 |
482206 |
1209477 |
26061564 |
294618682 |
721088889 |
67.0% |
0.2% |
0.2%
|
SRR1035750_1 |
36418326 |
29437479 |
80.8% |
1090003740 |
52580173 |
477676 |
1194376 |
25991217 |
292993343 |
716766955 |
66.9% |
0.2% |
0.2%
|
SRR1035751_1 |
37283288 |
30097060 |
80.7% |
1113232015 |
53583454 |
501012 |
1258616 |
26503728 |
299184745 |
732200460 |
66.9% |
0.2% |
0.2%
|
SRR1035752_1 |
37060706 |
29929057 |
80.8% |
1105518374 |
53252901 |
482131 |
1206278 |
26213632 |
296987990 |
727375442 |
67.0% |
0.2% |
0.2%
|
SRR1035753_1 |
36524684 |
29497226 |
80.8% |
1088783934 |
52383715 |
480767 |
1201878 |
25891164 |
292553540 |
716272870 |
66.9% |
0.2% |
0.2%
|
SRR1035754_1 |
44374421 |
35641925 |
80.3% |
1297737027 |
56550048 |
783384 |
1928227 |
33889478 |
345634464 |
858951426 |
62.5% |
0.2% |
0.2%
|
SRR1035755_1 |
47123418 |
38686887 |
82.1% |
1418615508 |
62395744 |
657788 |
1600283 |
37310750 |
378205898 |
938445045 |
62.6% |
0.2% |
0.2%
|
SRR1035756_1 |
46494325 |
38200717 |
82.2% |
1398750194 |
61544370 |
665506 |
1620058 |
36755277 |
372805600 |
925359383 |
62.6% |
0.2% |
0.2%
|
SRR1035757_1 |
33757685 |
27558529 |
81.6% |
1022678995 |
45970453 |
447518 |
1108988 |
27503711 |
273698575 |
673949750 |
62.6% |
0.2% |
0.2%
|
SRR1035758_1 |
51672955 |
43202041 |
83.6% |
1581348447 |
69853985 |
822137 |
1902495 |
41435007 |
421408587 |
1045926236 |
62.8% |
0.2% |
0.2%
|
SRR1035759_1 |
52552541 |
43875424 |
83.5% |
1603622609 |
70893193 |
835216 |
1927920 |
41918303 |
427271471 |
1060776506 |
62.8% |
0.2% |
0.2%
|
SRR1035760_1 |
52028953 |
43462815 |
83.5% |
1590035355 |
70151952 |
843868 |
1933038 |
41772663 |
423787545 |
1051546289 |
62.7% |
0.2% |
0.2%
|
SRR1035761_1 |
52203954 |
43546727 |
83.4% |
1591628706 |
70115005 |
830864 |
1912659 |
41792593 |
424214663 |
1052762922 |
62.7% |
0.2% |
0.2%
|
SRR1035762_1 |
51432756 |
42899477 |
83.4% |
1567397860 |
69243147 |
863158 |
1954416 |
41097046 |
417613231 |
1036626862 |
62.8% |
0.2% |
0.2%
|
SRR1035763_1 |
51936573 |
43290148 |
83.4% |
1581519608 |
69783508 |
841838 |
1914746 |
41424608 |
421377354 |
1046177554 |
62.8% |
0.2% |
0.2%
|
SRR1035764_1 |
41020260 |
33330224 |
81.3% |
1226993280 |
54818173 |
527463 |
1312101 |
32420376 |
327658331 |
810256836 |
62.8% |
0.2% |
0.2%
|
SRR1035765_1 |
41052812 |
33343513 |
81.2% |
1227624175 |
54908911 |
528111 |
1315673 |
32457666 |
327941036 |
810472778 |
62.8% |
0.2% |
0.2%
|
SRR1035766_1 |
40712660 |
33053039 |
81.2% |
1217077676 |
54307682 |
521433 |
1297309 |
32298209 |
325186448 |
803466595 |
62.7% |
0.2% |
0.2%
|
SRR1035767_1 |
41671785 |
33805763 |
81.1% |
1243572762 |
55361566 |
547813 |
1367520 |
32949551 |
332187811 |
821158501 |
62.7% |
0.2% |
0.2%
|
SRR1035768_1 |
41503242 |
33656899 |
81.1% |
1236709139 |
55086643 |
526393 |
1311440 |
32663075 |
330230911 |
816890677 |
62.8% |
0.2% |
0.2%
|
SRR1035769_1 |
40892220 |
33159591 |
81.1% |
1217419991 |
54160359 |
524999 |
1309045 |
32229531 |
325131538 |
804064519 |
62.7% |
0.2% |
0.2%
|
SRR1035770_1 |
46520916 |
36005366 |
77.4% |
1303239008 |
47706437 |
392006 |
922516 |
39617310 |
343379869 |
871220870 |
54.6% |
0.1% |
0.1%
|
SRR1035771_1 |
46414984 |
36467622 |
78.6% |
1321978264 |
48246698 |
365161 |
857484 |
40128827 |
348027507 |
884352587 |
54.6% |
0.1% |
0.1%
|
SRR1035772_1 |
46698438 |
36931175 |
79.1% |
1343232054 |
49132879 |
370344 |
880527 |
40949341 |
353897862 |
898001101 |
54.5% |
0.1% |
0.1%
|
SRR1035773_1 |
44515227 |
36654877 |
82.3% |
1335559941 |
49108711 |
338401 |
827107 |
40003144 |
350823734 |
894458844 |
55.1% |
0.1% |
0.1%
|
SRR1035774_1 |
47498272 |
38925077 |
82.0% |
1422251250 |
52656528 |
360868 |
883508 |
42309888 |
373729030 |
952311428 |
55.4% |
0.1% |
0.1%
|
SRR1035775_1 |
47993625 |
39338205 |
82.0% |
1428587161 |
53089619 |
361541 |
877516 |
42993840 |
376426283 |
954838362 |
55.3% |
0.1% |
0.1%
|
SRR1035776_1 |
46745030 |
38513176 |
82.4% |
1424830729 |
53136208 |
371102 |
891738 |
43254982 |
375890471 |
951286228 |
55.1% |
0.1% |
0.1%
|
SRR1035777_1 |
45500363 |
37600702 |
82.6% |
1397191787 |
52133415 |
362142 |
869751 |
42813494 |
368728979 |
932284006 |
54.9% |
0.1% |
0.1%
|
SRR1035778_1 |
46828689 |
38624177 |
82.5% |
1427434421 |
53057220 |
363400 |
875142 |
43281298 |
376483312 |
953374049 |
55.1% |
0.1% |
0.1%
|
SRR1035779_1 |
40595642 |
33420553 |
82.3% |
1227432100 |
45961822 |
340618 |
819171 |
37279212 |
324195235 |
818836042 |
55.2% |
0.1% |
0.1%
|
SRR1035780_1 |
62940191 |
48550487 |
77.1% |
1734872359 |
67573909 |
601959 |
1449099 |
51775843 |
456720838 |
1156750711 |
56.6% |
0.1% |
0.1%
|
SRR1035781_1 |
61291838 |
48240404 |
78.7% |
1727526315 |
67174823 |
555794 |
1344948 |
51445648 |
454514976 |
1152490126 |
56.6% |
0.1% |
0.1%
|
SRR1035782_1 |
63278424 |
49846622 |
78.8% |
1789904164 |
69646210 |
575617 |
1400533 |
53466326 |
471240194 |
1193575284 |
56.6% |
0.1% |
0.1%
|
SRR1035783_1 |
58831142 |
48192822 |
81.9% |
1730415712 |
68298140 |
522771 |
1307048 |
50748847 |
454461060 |
1155077846 |
57.4% |
0.1% |
0.1%
|
SRR1035784_1 |
63181484 |
51516939 |
81.5% |
1855959363 |
73800255 |
562998 |
1406647 |
54088183 |
487517361 |
1238583919 |
57.7% |
0.1% |
0.1%
|
SRR1035785_1 |
63692191 |
51886308 |
81.5% |
1856778254 |
74075763 |
560856 |
1400302 |
54675078 |
488855712 |
1237210543 |
57.5% |
0.1% |
0.1%
|
SRR1035786_1 |
62270233 |
51045276 |
82.0% |
1862011841 |
74460568 |
576038 |
1419385 |
55386423 |
491060518 |
1239108909 |
57.3% |
0.1% |
0.1%
|
SRR1035787_1 |
61085781 |
50245446 |
82.3% |
1842819779 |
73615572 |
567990 |
1398985 |
55370895 |
486406301 |
1225460036 |
57.1% |
0.1% |
0.1%
|
SRR1035788_1 |
62229996 |
51060158 |
82.1% |
1860220299 |
74205391 |
564944 |
1395963 |
55241189 |
490509785 |
1238303027 |
57.3% |
0.1% |
0.1%
|
SRR1035789_1 |
57247676 |
46746488 |
81.7% |
1687728750 |
67887659 |
552138 |
1369009 |
49936042 |
445135297 |
1122848605 |
57.6% |
0.1% |
0.1%
|
SRR1035790_1 |
60048643 |
44674883 |
74.4% |
1571276437 |
53613688 |
539622 |
1182691 |
73282698 |
441501621 |
1001156117 |
42.2% |
0.1% |
0.1%
|
SRR1035791_1 |
60008484 |
45273430 |
75.4% |
1594750385 |
54160775 |
507677 |
1110960 |
74281760 |
447715812 |
1016973401 |
42.2% |
0.1% |
0.1%
|
SRR1035792_1 |
60344165 |
45897611 |
76.1% |
1622389621 |
55261716 |
513085 |
1135739 |
75759300 |
455870110 |
1033849671 |
42.2% |
0.1% |
0.1%
|
SRR1035793_1 |
56610155 |
44702916 |
79.0% |
1581558605 |
54138085 |
467006 |
1057369 |
72917067 |
443343987 |
1009635091 |
42.6% |
0.1% |
0.1%
|
SRR1035794_1 |
60658563 |
47626463 |
78.5% |
1692216204 |
58275928 |
500954 |
1137191 |
77623550 |
474459104 |
1080219477 |
42.9% |
0.1% |
0.1%
|
SRR1035795_1 |
61384382 |
48200861 |
78.5% |
1702156127 |
58872375 |
500394 |
1129634 |
78928196 |
478633934 |
1084091594 |
42.7% |
0.1% |
0.1%
|
SRR1035796_1 |
59963818 |
47363964 |
79.0% |
1704764693 |
59269477 |
513609 |
1146552 |
79466441 |
479602081 |
1084766533 |
42.7% |
0.1% |
0.1%
|
SRR1035797_1 |
58279768 |
46215257 |
79.3% |
1669602625 |
58090464 |
501098 |
1119650 |
78285238 |
469865303 |
1061740872 |
42.6% |
0.1% |
0.1%
|
SRR1035798_1 |
60051400 |
47483827 |
79.1% |
1707250478 |
59095298 |
503536 |
1129531 |
79491057 |
480179307 |
1086851749 |
42.6% |
0.1% |
0.1%
|
SRR1035799_1 |
52596761 |
41408272 |
78.7% |
1476759415 |
51741276 |
475451 |
1059853 |
68681101 |
415804928 |
938996806 |
43.0% |
0.1% |
0.1%
|
SRR1035800_1 |
40106268 |
31755232 |
79.2% |
1137641163 |
49033401 |
726877 |
2266471 |
18271317 |
288229242 |
779113855 |
72.9% |
0.3% |
0.3%
|
SRR1035801_1 |
38488024 |
30360140 |
78.9% |
1088832548 |
47122295 |
705745 |
2193100 |
17417558 |
275958029 |
745435821 |
73.0% |
0.3% |
0.3%
|
SRR1035802_1 |
38314917 |
30299854 |
79.1% |
1086660774 |
47052939 |
697771 |
2174800 |
17422712 |
275409059 |
743903493 |
73.0% |
0.3% |
0.3%
|
SRR1035803_1 |
41585835 |
34657144 |
83.3% |
1242182200 |
53933305 |
789582 |
2497526 |
19538143 |
313445365 |
851978279 |
73.4% |
0.3% |
0.3%
|
SRR1035804_1 |
41907709 |
35044721 |
83.6% |
1264818547 |
55301550 |
801023 |
2533452 |
19972408 |
319645040 |
866565074 |
73.5% |
0.2% |
0.3%
|
SRR1035805_1 |
42481868 |
35583563 |
83.8% |
1283786245 |
56213416 |
854843 |
2683701 |
20250977 |
324547019 |
879236289 |
73.5% |
0.3% |
0.3%
|
SRR1035806_1 |
40154762 |
33255816 |
82.8% |
1203935588 |
52780268 |
768977 |
2428273 |
18703797 |
304277613 |
824976660 |
73.8% |
0.3% |
0.3%
|
SRR1035807_1 |
40597084 |
33087865 |
81.5% |
1184899980 |
50934561 |
759356 |
2389428 |
18651498 |
299618859 |
812546278 |
73.2% |
0.3% |
0.3%
|
SRR1035808_1 |
40186019 |
32908838 |
81.9% |
1178071557 |
50477627 |
750164 |
2358661 |
18690022 |
297951699 |
807843384 |
73.0% |
0.3% |
0.3%
|
SRR1035809_1 |
40623459 |
33250740 |
81.9% |
1190390779 |
51076376 |
761925 |
2389986 |
18942922 |
301164479 |
816055091 |
72.9% |
0.3% |
0.3%
|
SRR1035810_1 |
39990834 |
32610579 |
81.5% |
1163733467 |
49568904 |
748160 |
2353128 |
18469505 |
294189949 |
798403821 |
72.9% |
0.3% |
0.3%
|
SRR1035811_1 |
37687878 |
30499485 |
80.9% |
1121777555 |
50148392 |
754018 |
2324423 |
18159177 |
285469294 |
764922251 |
73.4% |
0.3% |
0.3%
|
SRR1035812_1 |
37092815 |
29651290 |
79.9% |
1091281965 |
48686971 |
736013 |
2270028 |
17659645 |
277746958 |
744182350 |
73.4% |
0.3% |
0.3%
|
SRR1035813_1 |
37006842 |
29880538 |
80.7% |
1101657858 |
49209692 |
728399 |
2250422 |
17946954 |
280517101 |
751005290 |
73.3% |
0.3% |
0.3%
|
SRR1035814_1 |
42536480 |
35583514 |
83.7% |
1285295375 |
56892581 |
819512 |
2573566 |
20537273 |
326018226 |
878454217 |
73.5% |
0.3% |
0.3%
|
SRR1035815_1 |
47913251 |
37367213 |
78.0% |
1351568540 |
56510811 |
610876 |
1776322 |
19489614 |
330817875 |
942363042 |
74.4% |
0.2% |
0.2%
|
SRR1035816_1 |
45586019 |
35438612 |
77.7% |
1283367630 |
53930902 |
591780 |
1712493 |
18455154 |
314245763 |
894431538 |
74.5% |
0.2% |
0.2%
|
SRR1035817_1 |
45422738 |
35373259 |
77.9% |
1280644485 |
53790475 |
584536 |
1696771 |
18425453 |
313629867 |
892517383 |
74.5% |
0.2% |
0.2%
|
SRR1035818_1 |
47604749 |
39174778 |
82.3% |
1420777243 |
59969839 |
634795 |
1867696 |
20141667 |
346582776 |
991580470 |
74.9% |
0.2% |
0.2%
|
SRR1035819_1 |
48062450 |
39675267 |
82.5% |
1448530940 |
61592989 |
646608 |
1896735 |
20599438 |
353873765 |
1009921405 |
74.9% |
0.2% |
0.2%
|
SRR1035820_1 |
48829014 |
40370534 |
82.7% |
1473078831 |
62703742 |
700167 |
2058108 |
20908853 |
359999045 |
1026708916 |
75.0% |
0.2% |
0.2%
|
SRR1035821_1 |
46628485 |
38099788 |
81.7% |
1395068403 |
59337067 |
622464 |
1830100 |
19543701 |
340777142 |
972957929 |
75.2% |
0.2% |
0.2%
|
SRR1035822_1 |
46731321 |
37564817 |
80.4% |
1360008475 |
56854712 |
616591 |
1809244 |
19306370 |
332407858 |
949013700 |
74.7% |
0.2% |
0.2%
|
SRR1035823_1 |
46424865 |
37490726 |
80.8% |
1356810843 |
56552413 |
609859 |
1787426 |
19389028 |
331625256 |
946846861 |
74.5% |
0.2% |
0.2%
|
SRR1035824_1 |
46947416 |
37892633 |
80.7% |
1371476627 |
57252705 |
621179 |
1815202 |
19646429 |
335274448 |
956866664 |
74.5% |
0.2% |
0.2%
|
SRR1035825_1 |
46189258 |
37125640 |
80.4% |
1339566025 |
55495422 |
610801 |
1792929 |
19182460 |
327260527 |
935223886 |
74.3% |
0.2% |
0.2%
|
SRR1035826_1 |
43605729 |
34734130 |
79.7% |
1290160854 |
56160956 |
625027 |
1795788 |
18800554 |
317469176 |
895309353 |
74.9% |
0.2% |
0.2%
|
SRR1035827_1 |
42861727 |
33688737 |
78.6% |
1252052960 |
54378357 |
609255 |
1755489 |
18247298 |
308133949 |
868928612 |
74.9% |
0.2% |
0.2%
|
SRR1035828_1 |
43056467 |
34177392 |
79.4% |
1272164341 |
55279756 |
605521 |
1739457 |
18652088 |
313193757 |
882693762 |
74.8% |
0.2% |
0.2%
|
SRR1035829_1 |
48984785 |
40436828 |
82.5% |
1477291324 |
63627780 |
664477 |
1930386 |
21243121 |
362337692 |
1027487868 |
75.0% |
0.2% |
0.2%
|
SRR1035830_1 |
122387500 |
96891517 |
79.2% |
3452957650 |
133743349 |
992458 |
2368277 |
126133211 |
966568346 |
2223152009 |
51.5% |
0.1% |
0.1%
|
SRR1035831_1 |
180936136 |
145570639 |
80.5% |
5240282995 |
193217687 |
1431458 |
3476566 |
190379841 |
1455856420 |
3395921023 |
50.4% |
0.1% |
0.1%
|
SRR1035832_1 |
172063603 |
138391453 |
80.4% |
4959929490 |
184214947 |
1376360 |
3312810 |
180630617 |
1379663795 |
3210730961 |
50.5% |
0.1% |
0.1%
|
SRR1035833_1 |
178680281 |
143631742 |
80.4% |
5158597742 |
192288295 |
1387654 |
3368543 |
187425692 |
1433913964 |
3340213594 |
50.6% |
0.1% |
0.1%
|
SRR1035834_1 |
171844758 |
136327563 |
79.3% |
4840431463 |
179394249 |
1287756 |
3137604 |
174068248 |
1343172401 |
3139371205 |
50.8% |
0.1% |
0.1%
|
SRR1035835_1 |
179429223 |
142409791 |
79.4% |
4894377322 |
225516712 |
1543866 |
4067121 |
121840525 |
1336643706 |
3204765392 |
64.9% |
0.1% |
0.1%
|
SRR1035836_1 |
176084120 |
140382021 |
79.7% |
4861035695 |
225046969 |
1570647 |
4114742 |
122269797 |
1329137440 |
3178896100 |
64.8% |
0.1% |
0.1%
|
SRR1035837_1 |
182109789 |
144869405 |
79.6% |
5021547782 |
232044194 |
1640418 |
4299062 |
125718350 |
1373981079 |
3283864679 |
64.9% |
0.1% |
0.1%
|
SRR1035838_1 |
175859200 |
140614099 |
80.0% |
4901029857 |
226616594 |
1567681 |
4114297 |
124240917 |
1342792911 |
3201697457 |
64.6% |
0.1% |
0.1%
|
SRR1035839_1 |
157787934 |
123250898 |
78.1% |
4374242400 |
204773680 |
1543512 |
3918027 |
116398451 |
1207633728 |
2839975002 |
63.8% |
0.1% |
0.1%
|
SRR1035840_1 |
97824299 |
80469426 |
82.3% |
2894981772 |
141005150 |
3192085 |
9361119 |
50638841 |
754533473 |
1936251104 |
73.6% |
0.4% |
0.5%
|
SRR1035841_1 |
100022884 |
82182965 |
82.2% |
2951581357 |
143527067 |
3246952 |
9547007 |
51412368 |
769003867 |
1974844096 |
73.6% |
0.4% |
0.5%
|
SRR1035842_1 |
165474210 |
135822388 |
82.1% |
4802310660 |
227708222 |
5179739 |
15370328 |
81761651 |
1242677784 |
3229612936 |
73.6% |
0.4% |
0.5%
|
SRR1035843_1 |
178375059 |
145625083 |
81.6% |
5127069862 |
240731101 |
5508578 |
16444052 |
86318881 |
1324573379 |
3453493871 |
73.6% |
0.4% |
0.5%
|
SRR1035844_1 |
168215760 |
137989290 |
82.0% |
4899346338 |
232492004 |
5304920 |
15747213 |
83613430 |
1269116986 |
3293071785 |
73.5% |
0.4% |
0.5%
|
SRR1035845_1 |
130831169 |
108279523 |
82.8% |
3918464372 |
190487688 |
4305112 |
12582952 |
69252470 |
1021199440 |
2620636710 |
73.3% |
0.4% |
0.5%
|
SRR1035846_1 |
155650620 |
126961137 |
81.6% |
4545809716 |
217407158 |
4951261 |
14574874 |
79706413 |
1182662126 |
3046507884 |
73.2% |
0.4% |
0.5%
|
SRR1035847_1 |
46402705 |
37414150 |
80.6% |
1361002175 |
42529128 |
442670 |
1144602 |
36905700 |
338937815 |
941042260 |
53.5% |
0.1% |
0.1%
|
SRR1035848_1 |
44470848 |
35755096 |
80.4% |
1302218749 |
40887927 |
435056 |
1123739 |
35323616 |
324365567 |
900082844 |
53.7% |
0.1% |
0.1%
|
SRR1035849_1 |
44567216 |
35856939 |
80.5% |
1305576765 |
40959218 |
428277 |
1112381 |
35409702 |
325303700 |
902363487 |
53.6% |
0.1% |
0.1%
|
SRR1035850_1 |
47702501 |
40503387 |
84.9% |
1475466276 |
46451051 |
468770 |
1241536 |
39567728 |
366037608 |
1021699583 |
54.0% |
0.1% |
0.1%
|
SRR1035851_1 |
48130504 |
41004456 |
85.2% |
1503434684 |
47696825 |
475687 |
1257048 |
40461779 |
373590885 |
1039952460 |
54.1% |
0.1% |
0.1%
|
SRR1035852_1 |
48774704 |
41628917 |
85.3% |
1525509197 |
48503619 |
529660 |
1406237 |
41008049 |
379228675 |
1054832957 |
54.2% |
0.1% |
0.1%
|
SRR1035853_1 |
46209098 |
38970631 |
84.3% |
1431616918 |
45434653 |
456911 |
1199912 |
38272114 |
355605022 |
990648306 |
54.3% |
0.1% |
0.1%
|
SRR1035854_1 |
46761580 |
38856655 |
83.1% |
1414108077 |
43934203 |
457182 |
1203107 |
38115189 |
351466112 |
978932284 |
53.5% |
0.1% |
0.1%
|
SRR1035855_1 |
46345393 |
38693434 |
83.5% |
1407878550 |
43627763 |
450119 |
1182287 |
38076673 |
349950254 |
974591454 |
53.4% |
0.1% |
0.1%
|
SRR1035856_1 |
46860681 |
39101101 |
83.4% |
1422642997 |
44146645 |
459497 |
1205535 |
38528576 |
353704120 |
984598624 |
53.4% |
0.1% |
0.1%
|
SRR1035857_1 |
46080860 |
38299638 |
83.1% |
1389567491 |
42760898 |
453102 |
1196362 |
37574992 |
345186737 |
962395400 |
53.2% |
0.1% |
0.1%
|
SRR1035858_1 |
43281701 |
35618472 |
82.3% |
1329238996 |
43301816 |
466967 |
1210378 |
36358668 |
332643286 |
915257881 |
54.4% |
0.1% |
0.1%
|
SRR1035859_1 |
42695473 |
34681508 |
81.2% |
1294930862 |
42060564 |
458259 |
1190656 |
35400769 |
324082908 |
891737706 |
54.3% |
0.1% |
0.1%
|
SRR1035860_1 |
42737999 |
35060188 |
82.0% |
1311273676 |
42667840 |
448514 |
1156875 |
35979569 |
328338326 |
902682552 |
54.3% |
0.1% |
0.1%
|
SRR1035861_1 |
48889832 |
41701373 |
85.3% |
1529623499 |
49250609 |
486507 |
1266616 |
41512356 |
381570751 |
1055536660 |
54.3% |
0.1% |
0.1%
|
SRR1035862_1 |
43652243 |
34384472 |
78.8% |
1193708416 |
50420818 |
4901337 |
17102564 |
16839254 |
280645348 |
823799095 |
75.0% |
1.7% |
2.0%
|
SRR1035863_1 |
78549163 |
60967800 |
77.6% |
2086186421 |
88328232 |
8778013 |
30528432 |
29878297 |
495689528 |
1432983919 |
74.7% |
1.7% |
2.1%
|
SRR1035864_1 |
73243529 |
58027811 |
79.2% |
2004600627 |
84222213 |
8211294 |
28717696 |
27514223 |
472357014 |
1383578187 |
75.4% |
1.7% |
2.0%
|
SRR1035865_1 |
74457408 |
57490402 |
77.2% |
1990871735 |
85148132 |
8403532 |
29089891 |
28187197 |
471167835 |
1368875148 |
75.1% |
1.8% |
2.1%
|
SRR1035866_1 |
72757668 |
60830122 |
83.6% |
2128051986 |
76251742 |
2224331 |
6264368 |
40629441 |
507925801 |
1494756303 |
65.2% |
0.4% |
0.4%
|
SRR1035867_1 |
74812203 |
61984312 |
82.9% |
2136723316 |
75760071 |
2228307 |
6259023 |
41103187 |
512824980 |
1498547748 |
64.8% |
0.4% |
0.4%
|
SRR1035868_1 |
83486707 |
69908845 |
83.7% |
2444847012 |
89915965 |
2643118 |
7400396 |
46548527 |
587548210 |
1710790796 |
65.9% |
0.4% |
0.4%
|
SRR1035869_1 |
41320147 |
34409470 |
83.3% |
1208339715 |
46459800 |
1320247 |
3579845 |
24212582 |
295213850 |
837553391 |
65.7% |
0.4% |
0.4%
|
SRR1035870_1 |
47789103 |
40924532 |
85.6% |
1425544489 |
46319030 |
1512034 |
4071687 |
36599577 |
349031146 |
988011015 |
55.9% |
0.4% |
0.4%
|
SRR1035871_1 |
61310358 |
50947605 |
83.1% |
1753501777 |
55877077 |
1915502 |
5118611 |
45692802 |
433076875 |
1211820910 |
55.0% |
0.4% |
0.4%
|
SRR1035872_1 |
69142773 |
59266825 |
85.7% |
2085664823 |
67892559 |
2234554 |
6083923 |
54079900 |
510788530 |
1444585357 |
55.7% |
0.4% |
0.4%
|
SRR1035873_1 |
19183882 |
16312251 |
85.0% |
567841318 |
18727861 |
603633 |
1625652 |
14465963 |
138857946 |
393560263 |
56.4% |
0.4% |
0.4%
|
SRR1035874_1 |
78862706 |
66882077 |
84.8% |
2301759629 |
75631206 |
2460088 |
6584233 |
59326462 |
564886601 |
1592871039 |
56.0% |
0.4% |
0.4%
|
SRR1035875_1 |
52679182 |
41593645 |
79.0% |
1434844681 |
60414839 |
2626612 |
8957240 |
17903363 |
340338475 |
1004604152 |
77.1% |
0.8% |
0.9%
|
SRR1035876_1 |
42830887 |
33753115 |
78.8% |
1174302962 |
49719721 |
2155155 |
7325554 |
14800889 |
279667353 |
820634290 |
77.1% |
0.8% |
0.9%
|
SRR1035877_1 |
85498668 |
66821419 |
78.2% |
2338028492 |
103484480 |
4480985 |
14830338 |
29742627 |
570720424 |
1614769638 |
77.7% |
0.8% |
0.9%
|
SRR1035878_1 |
95164282 |
71050862 |
74.7% |
2472481090 |
109251506 |
4777013 |
15492036 |
33057292 |
607226785 |
1702676458 |
76.8% |
0.8% |
0.9%
|
SRR1035879_1 |
160857256 |
121844324 |
75.7% |
4387616697 |
204827680 |
4165477 |
11273308 |
147288362 |
1249487995 |
2770573875 |
58.2% |
0.3% |
0.4%
|
SRR1035880_1 |
162610785 |
122398416 |
75.3% |
4409289994 |
205742900 |
4169412 |
11297511 |
148363331 |
1255642305 |
2784074535 |
58.1% |
0.3% |
0.4%
|
SRR1035881_1 |
122178695 |
91185010 |
74.6% |
3295540452 |
154931631 |
3113323 |
8422807 |
112007006 |
939022709 |
2078042976 |
58.0% |
0.3% |
0.4%
|
SRR1035882_1 |
118392394 |
93715052 |
79.2% |
3279344925 |
131219340 |
2680794 |
7854033 |
45130063 |
780262948 |
2312197747 |
74.4% |
0.3% |
0.3%
|
SRR1035883_1 |
96191682 |
75468112 |
78.5% |
2631230080 |
101130016 |
2156234 |
6482958 |
34568940 |
613453273 |
1873438659 |
74.5% |
0.4% |
0.3%
|
SRR1035884_1 |
118745673 |
91541752 |
77.1% |
3202677064 |
130072050 |
2947927 |
8611131 |
44239240 |
761040345 |
2255766371 |
74.6% |
0.4% |
0.4%
|
SRR1035885_1 |
74242906 |
63517801 |
85.6% |
2235564297 |
67291974 |
1744210 |
4646299 |
70944060 |
563506266 |
1527431488 |
48.7% |
0.3% |
0.3%
|
SRR1035886_1 |
127417108 |
109304663 |
85.8% |
3861416749 |
102241861 |
2930992 |
8334102 |
111399368 |
924600371 |
2711910055 |
47.9% |
0.3% |
0.3%
|
SRR1035887_1 |
131669941 |
112388271 |
85.4% |
4002848671 |
114341836 |
2973117 |
8149999 |
124720057 |
994309022 |
2758354640 |
47.8% |
0.3% |
0.3%
|
SRR1035888_1 |
86304659 |
71697120 |
83.1% |
2485016766 |
62769121 |
2271845 |
6206697 |
87373959 |
618332059 |
1708063085 |
41.8% |
0.4% |
0.4%
|
SRR1035889_1 |
127170770 |
108342009 |
85.2% |
3846945108 |
101343359 |
2805069 |
7363971 |
139291584 |
969400429 |
2626740696 |
42.1% |
0.3% |
0.3%
|
SRR1035890_1 |
119854663 |
101759415 |
84.9% |
3595709881 |
88725745 |
2560568 |
6955439 |
124142230 |
880809300 |
2492516599 |
41.7% |
0.3% |
0.3%
|
SRR1035891_1 |
91239997 |
74745248 |
81.9% |
2653614957 |
108388664 |
2146269 |
5526595 |
59730189 |
680506327 |
1797316913 |
64.5% |
0.3% |
0.3%
|
SRR1035892_1 |
126577102 |
103852068 |
82.0% |
3629689644 |
144390800 |
2934970 |
7846476 |
75558554 |
906300942 |
2492657902 |
65.6% |
0.3% |
0.3%
|
SRR1035893_1 |
111871350 |
93275476 |
83.4% |
3316187159 |
135223354 |
2983166 |
7759640 |
70107364 |
844289491 |
2255824144 |
65.9% |
0.4% |
0.3%
|
SRR1035894_1 |
140809291 |
100175988 |
71.1% |
3539413261 |
144646017 |
2467134 |
7141204 |
44663939 |
836046240 |
2504448727 |
76.4% |
0.3% |
0.3%
|
SRR1035895_1 |
95587884 |
64890746 |
67.9% |
2251742449 |
105473176 |
1989431 |
5274051 |
34333784 |
565817884 |
1538854123 |
75.4% |
0.4% |
0.3%
|
SRR1035896_1 |
82314087 |
54844741 |
66.6% |
1889983707 |
83000452 |
1631471 |
4522452 |
25774684 |
461578107 |
1313476541 |
76.3% |
0.4% |
0.3%
|
Bam to MethylFreq
MF to Wig
Bam to Hapinfo
TSCC-1: /home/ddiep/dinh_working/Bellvitge_BRI_WGBS/methylfiles/BAMfiles
TSCC-2: /oasis/tscc/scratch/ddiep/BAMfiles
Genome-miner: /media/LTS_60T/Dinh/WGBS_LTS33/Hg19/Estellar_Bellvitge/BAMfiles
cd /oasis/tscc/scratch/ddiep/BAMfiles
perl ~/bin/SaminfoPre4hapinfo.pl > ~/oasis/Estellar2016/SaminfoPre4hapinfo.txt
cd /home/shg047/oasis/Estellar2016/bam
perl ~/bin/bam2hapInfo2PBS.pl ../SaminfoPre4hapinfo.txt submit nonbismark
qsub SRX381621_tumor_breast.chr20.job
- Merge hapinfo in different chrosome to one file by sample ID
cd /home/shg047/oasis/Estellar2016/hapinfo
perl ~/bin/hapinfoMergeByChrosome.pl
cd /home/shg047/oasis/Estellar2016/mergeHapinfo
Haploinfo to Methylation Haplotype Block (MHB)
cd /home/shg047/oasis/Estellar2016/mergeHapinfo
cat *.hapInfo.txt >> HapinfoMerge.txt
perl ~/bin/hapinfo2mhb.pl HapinfoMerge.txt 0.4 > Heyn2016.R0.4.methyblock.bed
perl ~/bin/hapinfo2mhb.pl HapinfoMerge.txt 0.5 > Heyn2016.R0.5.methyblock.bed
perl ~/bin/hapinfo2mhb.pl HapinfoMerge.txt 0.6 > Heyn2016.R0.6.methyblock.bed
perl ~/bin/hapinfo2mhb.pl HapinfoMerge.txt 0.7 > Heyn2016.R0.7.methyblock.bed
qsub hapinfo2mhb.job
bedtools intersect -wa -u -a ../../monod/mhb/WGBS_pooled_mappable_bins.all_autosomes.mld_blocks_r2-0.5.bed -b Heyn2016.R0.5.methyblock.bed | wc -l
bedtools intersect -wa -u -a Heyn2016.R0.5.methyblock.bed -b ../../monod/mhb/WGBS_pooled_mappable_bins.all_autosomes.mld_blocks_r2-0.5.bed | wc -l
wc -l ../../monod/mhb/WGBS_pooled_mappable_bins.all_autosomes.mld_blocks_r2-0.5.bed
- 73976 Heyn2016.R0.5.methyblock.bed:File:Heyn2016.R0.5.methyblock.bed.txt
- 71697 of 147888 within Heyn2016.R0.5.methyblock.bed
- 73976 of Heyn2016.R0.5.methyblock.bed within 147888
- MHB identified by Heyn2016 dataset 100% located within our previous defined MHBs
Hapinfo to Methylation frequency(MF)
perl ~/bin/hapinfo2mf-Estellar.pl ./ > ../Estellar2016.hapinfo2mf.txt
Hapinfo to Methylation Haplotype Load
cd /home/shg047/oasis/Estellar2016/mergeHapinfo
perl ~/bin/hapinfo2mhl.pl ./ > Estellar2016.MHL.txt
qsub hapinfo2mhlPBS.job
* Estellar2016.MHL.txt
* 22 samples
* 147314 MHB
* missing ratio: 19.01826%
MHL