Perhaps I missed something, but is there a straightforward way to extract reads which span an exon/exon junction (ie, spliced reads) from the accepted_hits.bam produced by Tophat? I thought I could filter to find reads that have an alignment distance (alignment start - alignment end) greater than the read length, but the .bam file only lists the start position. Looking at the .bam file and the SAM specification, I didn't find a flag that is set which I could filter on.
Am I missing something?
Thanks!
Am I missing something?
Thanks!
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