Daniel:Notebook/Haplotyping/ReadCounts
Jump to navigation
Jump to search
Haplotyping-Read Counts[edit]
This page has the tables of read counts I've generated for each of the files. Read counts we generated using samtools idxstats on bam files.
Main Table[edit]
span | hic-reads | BAC-Reads | SISSOR-reads | PGP1-21 | PGP1-22 | |
chr1 | 249250621 | 78129185 | 110417582 | 5917328 | 3690528 | 2226800 |
chr2 | 243199373 | 86407296 | 133875940 | 6322513 | 3736040 | 2586473 |
chr3 | 198022430 | 73174690 | 112911067 | 5811622 | 2860856 | 2950766 |
chr4 | 191154276 | 70839026 | 125374491 | 4919271 | 3051617 | 1867654 |
chr5 | 180915260 | 65462467 | 106417397 | 4414255 | 2769597 | 1644658 |
chr6 | 171115067 | 62906486 | 97403294 | 3862673 | 2556119 | 1306554 |
chr7 | 159138663 | 53490808 | 83521080 | 4034191 | 2517684 | 1516507 |
chr8 | 146364022 | 51939936 | 79737177 | 3603627 | 2330827 | 1272800 |
chr9 | 141213431 | 38255793 | 61630613 | 2800289 | 1892797 | 907492 |
chr10 | 135534747 | 46002149 | 65089978 | 4299471 | 2029233 | 2270238 |
chr11 | 135006516 | 46649134 | 65813765 | 4059994 | 2271284 | 1788710 |
chr12 | 133851895 | 47090602 | 66670261 | 3428340 | 1904391 | 1523949 |
chr13 | 115169878 | 35384168 | 60278370 | 1837670 | 1287109 | 550561 |
chr14 | 107349540 | 30960402 | 46320540 | 2413738 | 1362037 | 1051701 |
chr15 | 102531392 | 27109654 | 38927528 | 2340534 | 1233518 | 1107016 |
chr16 | 90354753 | 23371040 | 30323820 | 2189239 | 1221961 | 967278 |
chr17 | 81195210 | 23122646 | 29365902 | 2514068 | 1120861 | 1393207 |
chr18 | 78077248 | 27685598 | 43339252 | 1832082 | 1117674 | 714408 |
chr19 | 59128983 | 13141030 | 13470108 | 2578232 | 859754 | 1718478 |
chr20 | 63025520 | 19473599 | 23435209 | 1521797 | 944285 | 577512 |
chr21 | 48129895 | 12566666 | 19371595 | 858885 | 503209 | 355676 |
chr22 | 51304566 | 8887960 | 9828415 | 998105 | 413696 | 584409 |
Total | 2881033286 | 942050335 | 1423523384 | 72557924 | 41675077 | 30882847 |
Coverage | 32.7 | 49.4 | 2.5 | 1.4 | 1.1 |
Files[edit]
- Hi-C:/oasis/tscc/scratch/sselvaraj/human_tissues/htissues/KZPGP1/fastq/hi-c/chr*/PGP1.final.chr*.corrected.bam
- BAC:/media/LTS_33T/KZ_LTS33T/PGP1_BacPool/fixed.bam/PGP1_****BacPool_Indx**.fixed.bam
- PGP1-21 (SISSOR):/media/LTS_15T/DEJ_LTS/microfluidics_data/pgp22/data_by_chamber/chamber***/chamber***_pgp1_21.BQSR.realigned.bam
- PGP1-22 (SISSOR):/media/LTS_15T/DEJ_LTS/microfluidics_data/pgp22/data_by_chamber/chamber***/pgp22_chamber***.BQSR.realigned.bam
- * chromsomes 1 to 22
- ** indexes 73 to 96, plus Indx85.2 and Indx92.2
- *** chambers 1 to 24
- **** 3 or 6