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.
I'm running the following command when it seg faults
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!
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
Code:
genomeCoverageBed -split -strand + -bg -ibam chr21_maternal.other.sort.bam -g hg18.txt > chr21_maternal.otherp.wig
Any ideas about what is going on? Has anyone ever come across this problem before?
Thanks!
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