Ns126:Encode Methylation: Difference between revisions
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*With above setting, the alignment time usage is about 16 hours | *With above setting, the alignment time usage is about 16 hours | ||
*The time is propotional to the size of the fastq file | *The time is propotional to the size of the fastq file | ||
{| {{table}} | {| {{table}} | ||
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| align="center" style="background:#f0f0f0;"|'''P(MCHH)''' | | align="center" style="background:#f0f0f0;"|'''P(MCHH)''' | ||
|- | |- | ||
| | | ENCFF000LVN||42665329||31372051||73.50%||227374577||9979920||566174||2568709||16516656||50531408||147211710||37.70%||1.10%||1.70% | ||
|- | |- | ||
| | | ENCFF000LWL||37938401||25076517||66.10%||232580318||11488185||403775||1382726||44058434||51038500||124208698||20.70%||0.80%||1.10% | ||
|- | |- | ||
| | | ENCFF000LVR||36779630||25226017||68.60%||216621540||12232832||438455||1846136||33041219||46480917||122581981||27.00%||0.90%||1.50% | ||
|- | |- | ||
| | | ENCFF000LVW||36169867||22446797||62.10%||224690704||12356273||372366||871608||41484525||51598506||118007426||22.90%||0.70%||0.70% | ||
|- | |- | ||
| | | ENCFF000LVB||35375019||22874896||64.70%||211937214||13517127||359167||1121727||31366464||47860817||117711912||30.10%||0.70%||0.90% | ||
|- | |- | ||
| | | ENCFF000LUP||34214415||20212548||59.10%||221862905||16119238||340947||580628||49637185||51949984||103234923||24.50%||0.70%||0.60% | ||
|- | |- | ||
| | | ENCFF000LWA||33924878||20895342||61.60%||226298397||14274674||319602||583229||52752860||53011846||105356186||21.30%||0.60%||0.60% | ||
|- | |- | ||
| | | ENCFF000LUV||33798173||23173663||68.60%||249630261||10489904||225941||428583||62372541||57063134||119050158||14.40%||0.40%||0.40% | ||
|- | |- | ||
| | | ENCFF000LWY||33715116||19999502||59.30%||213287381||13105506||316152||583822||46433586||48748868||104099447||22.00%||0.60%||0.60% | ||
|- | |- | ||
| | | ENCFF000LWW||33642793||20282649||60.30%||216267059||15823449||340126||638093||43292443||49869268||106303680||26.80%||0.70%||0.60% | ||
|- | |- | ||
| | | ENCFF000LWP||32858930||20654452||62.90%||219544115||13223974||319601||599593||48455363||50129553||106816031||21.40%||0.60%||0.60% | ||
|- | |- | ||
| | | ENCFF000LUU||32815340||17866807||54.40%||196534662||12582324||421909||799252||48097172||45287260||89346745||20.70%||0.90%||0.90% | ||
|- | |- | ||
| | | ENCFF000LVF||31276946||22130843||70.80%||241339808||11057578||348695||664774||64178792||55276052||109813917||14.70%||0.60%||0.60% | ||
|- | |- | ||
| | | ENCFF000LXB||29681695||14796658||49.90%||160388755||8182288||279840||480680||41788931||37024968||72632048||16.40%||0.80%||0.70% | ||
|- | |- | ||
| | | ENCFF000LWK||29349446||12860133||43.80%||137008343||8665157||302283||567461||29580229||31441673||66451540||22.70%||1.00%||0.80% | ||
|- | |- | ||
| | | ENCFF000LWE||29211774||11162094||38.20%||115410335||8071486||277005||511615||23863725||26859483||55827021||25.30%||1.00%||0.90% | ||
|- | |- | ||
| | | ENCFF000LVK||27335110||16938233||62.00%||193589572||12327753||322954||495345||51995628||43692466||84755426||19.20%||0.70%||0.60% | ||
|- | |- | ||
| | | ENCFF000LVO||26190075||19276422||73.60%||150096025||7012551||300245||1332640||19959469||31819734||89671386||26.00%||0.90%||1.50% | ||
|- | |- | ||
| | | ENCFF000LVA||25660341||16009728||62.40%||152217865||12748317||546338||1806399||26835875||36223859||74057077||32.20%||1.50%||2.40% | ||
|- | |- | ||
| ENCFF000LWD||25467744||15459206||60.70%||149205383||11335949||535669||1829440||30226946||34383379||70894000||27.30%||1.50%||2.50% | | ENCFF000LWD||25467744||15459206||60.70%||149205383||11335949||535669||1829440||30226946||34383379||70894000||27.30%||1.50%||2.50% | ||
|- | |- | ||
| | | ENCFF000LVU||23511285||15078397||64.10%||141659239||8631088||272002||734661||21915485||33328412||76777591||28.30%||0.80%||0.90% | ||
|- | |- | ||
| | | ENCFF000LWO||22844877||14206467||62.20%||153005363||9813445||247506||461786||33745829||35223721||73513076||22.50%||0.70%||0.60% | ||
|- | |- | ||
| | | ENCFF000LVI||22656883||13335953||58.90%||143634615||13714133||389619||650547||32241351||34451974||62186991||29.80%||1.10%||1.00% | ||
|- | |- | ||
| | | ENCFF000LUQ||22247066||13650824||61.40%||150112632||9777330||287617||504659||38167142||34898963||66476921||20.40%||0.80%||0.80% | ||
|- | |- | ||
| | | ENCFF000LUT||22240097||14849726||66.80%||162779228||9543204||285378||485629||41824570||38682843||71957604||18.60%||0.70%||0.70% | ||
|- | |- | ||
| | | ENCFF000LWH||21943620||12872848||58.70%||137662143||11585659||414164||781429||29526002||32473470||62881419||28.20%||1.30%||1.20% | ||
|- | |- | ||
| | | ENCFF000LVE||21473578||14519161||67.60%||157450743||7444292||221900||417095||40943018||36372568||72051870||15.40%||0.60%||0.60% | ||
|- | |- | ||
| | | ENCFF000LWX||21208447||13218301||62.30%||145215571||9668358||223882||356827||34200783||33840207||66925514||22.00%||0.70%||0.50% | ||
|- | |- | ||
| | | ENCFF000LVV||21080863||13197949||62.60%||142640926||10137634||255425||440789||32877645||33833167||65096266||23.60%||0.70%||0.70% | ||
|- | |- | ||
| | | ENCFF000MLE||20338545||12207095||60.00%||110465581||11201397||457519||1827464||19226614||25845153||51907434||36.80%||1.70%||3.40% | ||
|- | |- | ||
| | | ENCFF000LWS||20241908||11560661||57.10%||126245157||11387405||245297||424016||29669508||30429870||54089061||27.70%||0.80%||0.80% | ||
|- | |- | ||
| | | ENCFF000LVZ||20058311||11004008||54.90%||120506134||9791631||242794||448332||25470114||28547035||56006228||27.80%||0.80%||0.80% | ||
|- | |- | ||
| | | ENCFF000LWT||19407909||10887950||56.10%||119134111||9343415||203527||331921||25331949||28315688||55607611||26.90%||0.70%||0.60% | ||
|- | |- | ||
| | | ENCFF000MLD||19184685||14418868||75.20%||162604971||6716952||305536||587608||54429999||38467374||62097502||11.00%||0.80%||0.90% | ||
|- | |- | ||
| | | ENCFF000MLP||18102015||10032177||55.40%||109233809||10521402||215592||370895||25497472||26468867||46159581||29.20%||0.80%||0.80% | ||
|- | |- | ||
| | | ENCFF000LVJ||17856591||11324104||63.40%||102317536||8591993||307833||1097735||17653908||24511494||50154573||32.70%||1.20%||2.10% | ||
|- | |- | ||
| | | ENCFF000MLJ||16177211||8675428||53.60%||94678187||9430914||200777||318563||22135878||23265164||39326891||29.90%||0.90%||0.80% | ||
|- | |- | ||
| | | ENCFF000LUN||10913594||3643074||33.40%||40450477||3011262||76408||126647||9141529||9549119||18545512||24.80%||0.80%||0.70% | ||
|- | |- | ||
| | | ENCFF000MLM||5127779||2931330||57.20%||36675584||1281379||40172||75178||10725366||8687156||15866333||10.70%||0.50%||0.50% | ||
|- | |- | ||
| | | | ||
|} | |} |
Revision as of 20:04, 15 January 2016
RRBS Data Analysis to Encode Project
Aim
- Aim 1: methylation block with RRBS dataset
Background
- 1, Encode: http://genome.ucsc.edu/ENCODE/downloads.html
- 2, Encode|RRBS1: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibMethylRrbs/
- 3, Encode|RRBS2: http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=437674359_aUhx08DjchWwtBjyCYv61EB7Yy8S&c=chr1&g=wgEncodeHaibMethylRrbs
- big problem for the fastq files from the above link. 1) not fastq but rather RAS file 2) reads is not true reads.
- 4, Encode|Methy450K: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibMethyl450/
- 5, Encode|software: https://www.encodeproject.org/software/
Method
Data Download
Fastq and bed files can be downloaded from Encode Project. 101 RRBS data (bed files) were downloaded. 2,646,999 CpG loci were covered by 101 RRBS data while 866,979 CpG loci (32.8%) were detected in at least 80% samples.
Result
Alignment
- Maybe walltime time is too short , not all the samples were aligned completely, so I extend the walltime to 72 hours.
#PBS -q glean #PBS -l nodes=1:ppn=8 #PBS -l walltime=72:00:00 bismark --bowtie2 --phred64-quals --fastq -L 30 -N 1 --multicore 2 /home/shg047/db/hg19/meth/bismark ../fastq_trim/HOT197_trimmed.fq.gz -o ../bam2
- With above setting, the alignment time usage is about 16 hours
- The time is propotional to the size of the fastq file
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) |
ENCFF000LVN | 42665329 | 31372051 | 73.50% | 227374577 | 9979920 | 566174 | 2568709 | 16516656 | 50531408 | 147211710 | 37.70% | 1.10% | 1.70% |
ENCFF000LWL | 37938401 | 25076517 | 66.10% | 232580318 | 11488185 | 403775 | 1382726 | 44058434 | 51038500 | 124208698 | 20.70% | 0.80% | 1.10% |
ENCFF000LVR | 36779630 | 25226017 | 68.60% | 216621540 | 12232832 | 438455 | 1846136 | 33041219 | 46480917 | 122581981 | 27.00% | 0.90% | 1.50% |
ENCFF000LVW | 36169867 | 22446797 | 62.10% | 224690704 | 12356273 | 372366 | 871608 | 41484525 | 51598506 | 118007426 | 22.90% | 0.70% | 0.70% |
ENCFF000LVB | 35375019 | 22874896 | 64.70% | 211937214 | 13517127 | 359167 | 1121727 | 31366464 | 47860817 | 117711912 | 30.10% | 0.70% | 0.90% |
ENCFF000LUP | 34214415 | 20212548 | 59.10% | 221862905 | 16119238 | 340947 | 580628 | 49637185 | 51949984 | 103234923 | 24.50% | 0.70% | 0.60% |
ENCFF000LWA | 33924878 | 20895342 | 61.60% | 226298397 | 14274674 | 319602 | 583229 | 52752860 | 53011846 | 105356186 | 21.30% | 0.60% | 0.60% |
ENCFF000LUV | 33798173 | 23173663 | 68.60% | 249630261 | 10489904 | 225941 | 428583 | 62372541 | 57063134 | 119050158 | 14.40% | 0.40% | 0.40% |
ENCFF000LWY | 33715116 | 19999502 | 59.30% | 213287381 | 13105506 | 316152 | 583822 | 46433586 | 48748868 | 104099447 | 22.00% | 0.60% | 0.60% |
ENCFF000LWW | 33642793 | 20282649 | 60.30% | 216267059 | 15823449 | 340126 | 638093 | 43292443 | 49869268 | 106303680 | 26.80% | 0.70% | 0.60% |
ENCFF000LWP | 32858930 | 20654452 | 62.90% | 219544115 | 13223974 | 319601 | 599593 | 48455363 | 50129553 | 106816031 | 21.40% | 0.60% | 0.60% |
ENCFF000LUU | 32815340 | 17866807 | 54.40% | 196534662 | 12582324 | 421909 | 799252 | 48097172 | 45287260 | 89346745 | 20.70% | 0.90% | 0.90% |
ENCFF000LVF | 31276946 | 22130843 | 70.80% | 241339808 | 11057578 | 348695 | 664774 | 64178792 | 55276052 | 109813917 | 14.70% | 0.60% | 0.60% |
ENCFF000LXB | 29681695 | 14796658 | 49.90% | 160388755 | 8182288 | 279840 | 480680 | 41788931 | 37024968 | 72632048 | 16.40% | 0.80% | 0.70% |
ENCFF000LWK | 29349446 | 12860133 | 43.80% | 137008343 | 8665157 | 302283 | 567461 | 29580229 | 31441673 | 66451540 | 22.70% | 1.00% | 0.80% |
ENCFF000LWE | 29211774 | 11162094 | 38.20% | 115410335 | 8071486 | 277005 | 511615 | 23863725 | 26859483 | 55827021 | 25.30% | 1.00% | 0.90% |
ENCFF000LVK | 27335110 | 16938233 | 62.00% | 193589572 | 12327753 | 322954 | 495345 | 51995628 | 43692466 | 84755426 | 19.20% | 0.70% | 0.60% |
ENCFF000LVO | 26190075 | 19276422 | 73.60% | 150096025 | 7012551 | 300245 | 1332640 | 19959469 | 31819734 | 89671386 | 26.00% | 0.90% | 1.50% |
ENCFF000LVA | 25660341 | 16009728 | 62.40% | 152217865 | 12748317 | 546338 | 1806399 | 26835875 | 36223859 | 74057077 | 32.20% | 1.50% | 2.40% |
ENCFF000LWD | 25467744 | 15459206 | 60.70% | 149205383 | 11335949 | 535669 | 1829440 | 30226946 | 34383379 | 70894000 | 27.30% | 1.50% | 2.50% |
ENCFF000LVU | 23511285 | 15078397 | 64.10% | 141659239 | 8631088 | 272002 | 734661 | 21915485 | 33328412 | 76777591 | 28.30% | 0.80% | 0.90% |
ENCFF000LWO | 22844877 | 14206467 | 62.20% | 153005363 | 9813445 | 247506 | 461786 | 33745829 | 35223721 | 73513076 | 22.50% | 0.70% | 0.60% |
ENCFF000LVI | 22656883 | 13335953 | 58.90% | 143634615 | 13714133 | 389619 | 650547 | 32241351 | 34451974 | 62186991 | 29.80% | 1.10% | 1.00% |
ENCFF000LUQ | 22247066 | 13650824 | 61.40% | 150112632 | 9777330 | 287617 | 504659 | 38167142 | 34898963 | 66476921 | 20.40% | 0.80% | 0.80% |
ENCFF000LUT | 22240097 | 14849726 | 66.80% | 162779228 | 9543204 | 285378 | 485629 | 41824570 | 38682843 | 71957604 | 18.60% | 0.70% | 0.70% |
ENCFF000LWH | 21943620 | 12872848 | 58.70% | 137662143 | 11585659 | 414164 | 781429 | 29526002 | 32473470 | 62881419 | 28.20% | 1.30% | 1.20% |
ENCFF000LVE | 21473578 | 14519161 | 67.60% | 157450743 | 7444292 | 221900 | 417095 | 40943018 | 36372568 | 72051870 | 15.40% | 0.60% | 0.60% |
ENCFF000LWX | 21208447 | 13218301 | 62.30% | 145215571 | 9668358 | 223882 | 356827 | 34200783 | 33840207 | 66925514 | 22.00% | 0.70% | 0.50% |
ENCFF000LVV | 21080863 | 13197949 | 62.60% | 142640926 | 10137634 | 255425 | 440789 | 32877645 | 33833167 | 65096266 | 23.60% | 0.70% | 0.70% |
ENCFF000MLE | 20338545 | 12207095 | 60.00% | 110465581 | 11201397 | 457519 | 1827464 | 19226614 | 25845153 | 51907434 | 36.80% | 1.70% | 3.40% |
ENCFF000LWS | 20241908 | 11560661 | 57.10% | 126245157 | 11387405 | 245297 | 424016 | 29669508 | 30429870 | 54089061 | 27.70% | 0.80% | 0.80% |
ENCFF000LVZ | 20058311 | 11004008 | 54.90% | 120506134 | 9791631 | 242794 | 448332 | 25470114 | 28547035 | 56006228 | 27.80% | 0.80% | 0.80% |
ENCFF000LWT | 19407909 | 10887950 | 56.10% | 119134111 | 9343415 | 203527 | 331921 | 25331949 | 28315688 | 55607611 | 26.90% | 0.70% | 0.60% |
ENCFF000MLD | 19184685 | 14418868 | 75.20% | 162604971 | 6716952 | 305536 | 587608 | 54429999 | 38467374 | 62097502 | 11.00% | 0.80% | 0.90% |
ENCFF000MLP | 18102015 | 10032177 | 55.40% | 109233809 | 10521402 | 215592 | 370895 | 25497472 | 26468867 | 46159581 | 29.20% | 0.80% | 0.80% |
ENCFF000LVJ | 17856591 | 11324104 | 63.40% | 102317536 | 8591993 | 307833 | 1097735 | 17653908 | 24511494 | 50154573 | 32.70% | 1.20% | 2.10% |
ENCFF000MLJ | 16177211 | 8675428 | 53.60% | 94678187 | 9430914 | 200777 | 318563 | 22135878 | 23265164 | 39326891 | 29.90% | 0.90% | 0.80% |
ENCFF000LUN | 10913594 | 3643074 | 33.40% | 40450477 | 3011262 | 76408 | 126647 | 9141529 | 9549119 | 18545512 | 24.80% | 0.80% | 0.70% |
ENCFF000MLM | 5127779 | 2931330 | 57.20% | 36675584 | 1281379 | 40172 | 75178 | 10725366 | 8687156 | 15866333 | 10.70% | 0.50% | 0.50% |