Daniel:Notebook/Haplotyping/ReadCounts

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Haplotyping-Read Counts[edit]

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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