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Old 04-26-2012, 11:40 AM   #1
duhaimj
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Location: Montreal

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Default Tophat2: bam file has no quality sequences for a lot of reads

  • With the version 2 of tophat I get an '*' as quality sequences in the bam file for more that 70% of the reads.

    Ex:
    Read 1
    GCCCTCGCGGTGCTCTCCGGGTCTGTGCTGAGGAGAACGCAACTCCGCCG DDDDDDDFFFGHHHJJIJIJIIIJJIGGHIGJJJJJJHGHHHFFFFFCC@
    Read 2
    GGCGTGTGTTGC *
    Read 3
    CCGGCCCTCGCTCCAGCAGCTGGACCCCTACCTGCCGTCTGCTGC *

    Read 4
    CAACTGCTGGCCTGTGCCAGGGTGCAAGCTGAGCACTGGAGTGGAGTTTTC C@CFFFFFHGHHHIGHJJIIJICEHIGIIIIGHJGIJJJBGDFGGHHIIIH

    The bam file for this same sample with tophat 1.4 is ok.

    Has someone encountered this problem? THank you
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Old 04-26-2012, 02:40 PM   #2
Jon_Keats
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Default

Why are your read lengths different. Looks like the two that are the same size have proper quality strings
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Old 04-26-2012, 04:08 PM   #3
pzumbo
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I encountered the same problem.
Problem was alleviated by switching back to 1.4.1.
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Old 04-27-2012, 05:10 AM   #4
duhaimj
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My reads were filtered for quality. But the same problems happens without filtering. And version 1.4 corrects the problem as mentionned by pzumbo.
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Old 04-28-2012, 07:47 AM   #5
caddymob
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I'm having the same issue with tophat2. I just posted over here: http://seqanswers.com/forums/showpos...66&postcount=4
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