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