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  • 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.

  • #2
    It doesn't complain about the genome file, but about your BAM file. You should give the command with "-ibam [you_bam_file]" instead...

    Comment


    • #3
      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?

      Comment


      • #4
        ./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...

        Comment


        • #5
          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.

          Comment

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