Filtering a Tophat BAM file
Dear All,
I have a BAM file after Tophat2. When I checked it on Artemis after gene prediction using exon, intron and exon-intron combined, I saw some un specific exon-intron junctions. Also Augustus included very far exons into the same gene. I need to filter some RNAseq reads.
My questions are:
- which parameters should I modify on Tophat?
- Which reads should be removed?
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