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Our short Illumina reads appear to have varying lengths of adapter oligo at the 3' end.
Using bowtie I can use either '-l 20' to set the seedlength or '-trim3 16' to ignore 16 bases at the 3' end when doing alignments. There doesn't appear to be any way to do with same thing with tophat.
How do people handle this when running tophat? Should I just truncate all the reads to 20 bases before passing them to tophat?
Thanks in advance.
Using bowtie I can use either '-l 20' to set the seedlength or '-trim3 16' to ignore 16 bases at the 3' end when doing alignments. There doesn't appear to be any way to do with same thing with tophat.
How do people handle this when running tophat? Should I just truncate all the reads to 20 bases before passing them to tophat?
Thanks in advance.
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