Genome files for BEDTools GenomeCoverage command

qnc · 10-24-2011, 08:00 AM

Hi trying to get the BEDTools genomeCoverage working

$ ./genomeCoverageBed -i test.bam -g human.hg19.genome
It looks as though you have less than 3 columns at line: 1. Are you sure your files are tab-delimited?

The BAM files only covers the long arm of Chr22 would I have to set up the Genome File differently only for that section rather than the one provided in the BEDTools distribution genomes folder which has the following info:

$ more human.hg19.genome
chr1 249250621
chr2 243199373
chr3 198022430
chr4 191154276
chr5 180915260
chr6 171115067
chr7 159138663
chrX 155270560
chr8 146364022
chr9 141213431
chr10 135534747
chr11 135006516
chr12 133851895
chr13 115169878
chr14 107349540
chr15 102531392
chr16 90354753
chr17 81195210
chr18 78077248
chr20 63025520
chrY 59373566
chr19 59128983
chr22 51304566
chr21 48129895
chr6_ssto_hap7 4928567
chr6_mcf_hap5 4833398
chr6_cox_hap2 4795371
chr6_mann_hap4 4683263
chr6_apd_hap1 4622290
chr6_qbl_hap6 4611984
chr6_dbb_hap3 4610396
chr17_ctg5_hap1 1680828
chr4_ctg9_hap1 590426
chr1_gl000192_random 547496
chrUn_gl000225 211173
chr4_gl000194_random 191469
chr4_gl000193_random 189789
chr9_gl000200_random 187035
chrUn_gl000222 186861
chrUn_gl000212 186858
chr7_gl000195_random 182896
chrUn_gl000223 180455
chrUn_gl000224 179693
chrUn_gl000219 179198
chr17_gl000205_random 174588
chrUn_gl000215 172545
chrUn_gl000216 172294
chrUn_gl000217 172149
chr9_gl000199_random 169874
chrUn_gl000211 166566
chrUn_gl000213 164239
chrUn_gl000220 161802
chrUn_gl000218 161147
chr19_gl000209_random 159169
chrUn_gl000221 155397
chrUn_gl000214 137718
chrUn_gl000228 129120
chrUn_gl000227 128374
chr1_gl000191_random 106433
chr19_gl000208_random 92689
chr9_gl000198_random 90085
chr17_gl000204_random 81310
chrUn_gl000233 45941
chrUn_gl000237 45867
chrUn_gl000230 43691
chrUn_gl000242 43523
chrUn_gl000243 43341
chrUn_gl000241 42152
chrUn_gl000236 41934
chrUn_gl000240 41933
chr17_gl000206_random 41001
chrUn_gl000232 40652
chrUn_gl000234 40531
chr11_gl000202_random 40103
chrUn_gl000238 39939
chrUn_gl000244 39929
chrUn_gl000248 39786
chr8_gl000196_random 38914
chrUn_gl000249 38502
chrUn_gl000246 38154
chr17_gl000203_random 37498
chr8_gl000197_random 37175
chrUn_gl000245 36651
chrUn_gl000247 36422
chr9_gl000201_random 36148
chrUn_gl000235 34474
chrUn_gl000239 33824
chr21_gl000210_random 27682
chrUn_gl000231 27386
chrUn_gl000229 19913
chrM 16571
chrUn_gl000226 15008
chr18_gl000207_random 4262

Thanks for any points.

arvid · 10-24-2011, 11:43 PM

It doesn't complain about the genome file, but about your BAM file. You should give the command with "-ibam [you_bam_file]" instead...

qnc · 10-25-2011, 05:04 AM

Thanks its is working now But how do I get a report from its run that can be loaded into UCSC as a histogram track so I can see the coverage of the BAM file.

I tried this but it didn't work?

$ ./genomeCoverageBed -ibam test.bam -g human.hg19.genome -bg testBamHisto.BedGraph

This one give:

$ ./genomeCoverageBed -ibam test.bam -g human.hg19.genome
chr22 0 46231768 51304566 0.901124
chr22 1 497880 51304566 0.0097044
chr22 2 182566 51304566 0.00355847

SO presume its working its just to get the right output command?

arvid · 10-25-2011, 05:07 AM

./genomeCoverageBed -ibam test.bam -g human.hg19.genome -bg > testBamHisto.BedGraph

is what you want. I don't use the UCSC browser, but if you can display BedGraph on it, that should be it. It works fine with IGV for me...

qnc · 10-25-2011, 05:30 AM

LOL Ok it has made the file now I'll need to ask a UCSC expert about the look of it.

Wanted the Histogram view rather than the actual numbers?

More research required but thanks, learning a lot of useful stuff here.

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10-24-2011, 08:00 AM	#1
qnc Member Location: London Join Date: Jun 2010 Posts: 51	Genome files for BEDTools GenomeCoverage command Hi trying to get the BEDTools genomeCoverage working $ ./genomeCoverageBed -i test.bam -g human.hg19.genome It looks as though you have less than 3 columns at line: 1. Are you sure your files are tab-delimited? The BAM files only covers the long arm of Chr22 would I have to set up the Genome File differently only for that section rather than the one provided in the BEDTools distribution genomes folder which has the following info: $ more human.hg19.genome chr1 249250621 chr2 243199373 chr3 198022430 chr4 191154276 chr5 180915260 chr6 171115067 chr7 159138663 chrX 155270560 chr8 146364022 chr9 141213431 chr10 135534747 chr11 135006516 chr12 133851895 chr13 115169878 chr14 107349540 chr15 102531392 chr16 90354753 chr17 81195210 chr18 78077248 chr20 63025520 chrY 59373566 chr19 59128983 chr22 51304566 chr21 48129895 chr6_ssto_hap7 4928567 chr6_mcf_hap5 4833398 chr6_cox_hap2 4795371 chr6_mann_hap4 4683263 chr6_apd_hap1 4622290 chr6_qbl_hap6 4611984 chr6_dbb_hap3 4610396 chr17_ctg5_hap1 1680828 chr4_ctg9_hap1 590426 chr1_gl000192_random 547496 chrUn_gl000225 211173 chr4_gl000194_random 191469 chr4_gl000193_random 189789 chr9_gl000200_random 187035 chrUn_gl000222 186861 chrUn_gl000212 186858 chr7_gl000195_random 182896 chrUn_gl000223 180455 chrUn_gl000224 179693 chrUn_gl000219 179198 chr17_gl000205_random 174588 chrUn_gl000215 172545 chrUn_gl000216 172294 chrUn_gl000217 172149 chr9_gl000199_random 169874 chrUn_gl000211 166566 chrUn_gl000213 164239 chrUn_gl000220 161802 chrUn_gl000218 161147 chr19_gl000209_random 159169 chrUn_gl000221 155397 chrUn_gl000214 137718 chrUn_gl000228 129120 chrUn_gl000227 128374 chr1_gl000191_random 106433 chr19_gl000208_random 92689 chr9_gl000198_random 90085 chr17_gl000204_random 81310 chrUn_gl000233 45941 chrUn_gl000237 45867 chrUn_gl000230 43691 chrUn_gl000242 43523 chrUn_gl000243 43341 chrUn_gl000241 42152 chrUn_gl000236 41934 chrUn_gl000240 41933 chr17_gl000206_random 41001 chrUn_gl000232 40652 chrUn_gl000234 40531 chr11_gl000202_random 40103 chrUn_gl000238 39939 chrUn_gl000244 39929 chrUn_gl000248 39786 chr8_gl000196_random 38914 chrUn_gl000249 38502 chrUn_gl000246 38154 chr17_gl000203_random 37498 chr8_gl000197_random 37175 chrUn_gl000245 36651 chrUn_gl000247 36422 chr9_gl000201_random 36148 chrUn_gl000235 34474 chrUn_gl000239 33824 chr21_gl000210_random 27682 chrUn_gl000231 27386 chrUn_gl000229 19913 chrM 16571 chrUn_gl000226 15008 chr18_gl000207_random 4262 Thanks for any points.

10-24-2011, 11:43 PM	#2
arvid Senior Member Location: Berlin Join Date: Jul 2011 Posts: 156	It doesn't complain about the genome file, but about your BAM file. You should give the command with "-ibam [you_bam_file]" instead...

10-25-2011, 05:04 AM	#3
qnc Member Location: London Join Date: Jun 2010 Posts: 51	Thanks its is working now But how do I get a report from its run that can be loaded into UCSC as a histogram track so I can see the coverage of the BAM file. I tried this but it didn't work? $ ./genomeCoverageBed -ibam test.bam -g human.hg19.genome -bg testBamHisto.BedGraph This one give: $ ./genomeCoverageBed -ibam test.bam -g human.hg19.genome chr22 0 46231768 51304566 0.901124 chr22 1 497880 51304566 0.0097044 chr22 2 182566 51304566 0.00355847 SO presume its working its just to get the right output command?

10-25-2011, 05:07 AM	#4
arvid Senior Member Location: Berlin Join Date: Jul 2011 Posts: 156	./genomeCoverageBed -ibam test.bam -g human.hg19.genome -bg > testBamHisto.BedGraph is what you want. I don't use the UCSC browser, but if you can display BedGraph on it, that should be it. It works fine with IGV for me...

10-25-2011, 05:30 AM	#5
qnc Member Location: London Join Date: Jun 2010 Posts: 51	LOL Ok it has made the file now I'll need to ask a UCSC expert about the look of it. Wanted the Histogram view rather than the actual numbers? More research required but thanks, learning a lot of useful stuff here.