Filtering a Tophat BAM file

Question

[Mehmet]

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:

1. which parameters should I modify on Tophat?
2. Which reads should be removed?