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  • noms
    Junior Member
    • Apr 2012
    • 7

    #1

    Weird Seg Fault in Bedtools

    I'm getting a Seg Fault using genomeCoverageBed from the BEDtools package and I'm running out of ideas about what the cause is.

    I have narrowed down the problem to a couple of reads in my SAM file, before I convert it into BAM and index it.

    Code:
    @SQ     SN:chr21        LN:46944323
    TUPAC_0006:1:52:2620:5624#0     99      chr21   0       255     4I72M   =       18852856        142     TTATTTAAGTATTCAACTTTGTCCAAAGGATGTAGACNTGTATTAGGAGACATAATAAAATATTATCAATAATAAT    gggeggggggggggcgggggggggdgggggfggggdeBee`deedgcfgggggaegegeggeegggggggfeggcg    NH:i:1  HI:i:1  AS:i:149        nM:i:0  jM:B:c,-1
    TUPAC_0006:2:27:16247:2980#0    99      chr21   0       255     4I72M   =       18852856        142     TTATTTAAGTATTCAACTTTGTCCAAAGGATGTAGACCTGTATTAGGAGACATAATAAAATATTATCAATAATAAT    Yggfgc`fffgfadfggggggggfgdf]fffffffccdee]Wfffggagcdca_f_faccf`cafggggcfdfd[f    NH:i:1  HI:i:1  AS:i:150        nM:i:0  jM:B:c,-1
    I'm running the following command when it seg faults

    Code:
    genomeCoverageBed -split -strand + -bg -ibam chr21_maternal.other.sort.bam -g hg18.txt > chr21_maternal.otherp.wig
    And the code doesn't seg fault when only one of these reads are analyzed.
    Any ideas about what is going on? Has anyone ever come across this problem before?

    Thanks!
  • noms
    Junior Member
    • Apr 2012
    • 7

    #2
    Nevermind. Just realized that the starting position is zero.

    Comment

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