Aligned to mm10 using bowtie2, and converted to a sorted bam using samtools. How do I analyze my reads and what transcripts they correspond to
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Originally posted by westerman View PostI'd drop the bowtie2 and instead use Tophat2 (which granted, will use bowtie2 internally but will also do better analysis).
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Originally posted by KnowNothing2 View PostI had a question about that. Does bowtie2 throw reads out if they overlap at a splice junction since you're referencing to a genome ?
I point out that Tophat2 does not use '--local' but rather '--end-to-end'. It can do this because it actually splits up reads into smaller segments that should map end-to-end and not need the soft-clipping that 'local' generates.
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