Entering edit mode
7.8 years ago
komal.yasmin
▴
10
I am using the command
bedtools multicov [OPTIONS] -bams BAM1 BAM2 BAM3 ... BAMn -bed <bed gff="" vcf="">
for the bedtools to get the count matrix and the output I get is like this :
chr4 251355 266500 CG1674-RB 0 + 252579 266389 0 11 166,43,570,81,81,81,291,85,320,115,695, 0,1205,1549,3535,4134,5665,6539,9584,12536,12904,14450, 801
chr4 252055 266500 CG1674-RC 0 + 252579 266389 0 9 198,43,81,81,291,85,320,115,695, 0,505,2835,4965,5839,8884,11836,12204,13750, 785
chr4 252108 265205 CG1674-RA 0 + 252579 264217 0 12 122,43,570,81,81,291,117,85,138,219,483,162, 0,452,796,2782,4912,5786,7639,8831,9213,10978,11783,12935, 600
chr4 380577 395610 CG1710-RC 0 + 381316 393018 0 13 24,420,310,212,189,146,1074,1089,238,155,267,364,2735, 0,635,2352,2719,2994,3542,3916,5722,9555,9858,11139,11861,12298, 1625
chr4 380587 395610 CG1710-RB 0 + 381316 393018 0 13 19,420,310,212,189,146,1074,1089,238,155,267,364,2735, 0,625,2342,2709,2984,3532,3906,5712,9545,9848,11129,11851,12288, 1625
chr4 380602 395610 CG1710-RD 0 + 381316 393018 0 13 43,420,310,212,189,146,1074,1089,238,155,267,364,2735, 0,610,2327,2694,2969,3517,3891,5697,9530,9833,11114,11836,12273, 1625
chr4 380602 395610 CG1710-RA 0 + 381316 393018 0 13 308,420,310,212,189,146,1074,1089,238,155,267,364,2735, 0,610,2327,2694,2969,3517,3891,5697,9530,9833,11114,11836,12273, 1625
chr4 650318 655978 CG1732-RA 0 + 650461 655137 0 10 287,268,102,181,268,104,370,204,168,943, 0,1934,2335,2515,2755,3636,3798,4228,4484,4717, 4
chr4 650318 655978 CG1732-RB 0 + 650461 654676 0 10 287,268,102,181,268,104,370,164,168,943, 0,1934,2335,2515,2755,3636,3798,4268,4484,4717, 4
chr4 745029 796720 CG32019-RC 0 + 746342 796175 0 41 88,361,22,163,142,224,403,674,348,45,123,60,99,309,126,39,228,174,36,148,374,126,700,354,1713,900,764,136,891,2673,282,300,9471,979,342,1043,57,101,127,303,1180, 0,1265,2258,3057,3700,6373,6659,7156,8813,9516,9875,10074,10310,11111,11501,11745,12415,13332,14549,17999,18384,20762,20968,22072,22903,26166,27773,28621,28934,29883,33117,33461,33816,43358,44400,46149,47999,49613,49781,49973,50511, 2
chr4 745029 796720 CG32019-RD 0 + 746342 796175 0 46 88,361,22,163,142,133,201,302,224,403,674,348,45,123,60,99,309,126,39,177,228,174,36,33,148,374,126,700,354,1713,900,764,136,891,2673,282,300,9471,979,342,1043,57,101,127,303,1180, 0,1265,2258,3057,3700,4278,4598,4870,6373,6659,7156,8813,9516,9875,10074,10310,11111,11501,11745,11935,12415,13332,14549,15545,17999,18384,20762,20968,22072,22903,26166,27773,28621,28934,29883,33117,33461,33816,43358,44400,46149,47999,49613,49781,49973,50511, 2
I am using it for one bam file at a time and the bed file was downloaded from ucsc. I was expecting something like the count matrix generated by ht-seq. Is this output correct? (I am using default options)