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Old 10-24-2011, 07:00 AM   #1
qnc
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Default 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.
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Old 10-24-2011, 10:43 PM   #2
arvid
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It doesn't complain about the genome file, but about your BAM file. You should give the command with "-ibam [you_bam_file]" instead...
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Old 10-25-2011, 04:04 AM   #3
qnc
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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?
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Old 10-25-2011, 04:07 AM   #4
arvid
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./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...
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Old 10-25-2011, 04:30 AM   #5
qnc
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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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