Filter single exon reads

Question

[sloux]

I used Trinity to create a fasta file for my transcriptome, which I then mapped to the genome. Unfortunately, there are a lot of single exon reads in the BAM file which appear to just be junk. Does anyone know of a good way to filter these out? I can do it manually, but I really don't want to do that for a full BAM file.

[GenoMax]

there are a lot of single exon reads

What exactly does that mean?

[sloux]

There are single exon reads I want to remove from my BAM file, i.e. they don't have splice sites. Many of them appear to be pre-mRNA, or intronic reads which I don't want in my final file.

[GenoMax]

Take a look at this: A: Filtering out the spliced reads from bam file. You want the opposite of what is being asked there.

See if reformat.sh in=mapped.bam out=filtered.bam maxdellen=0 does what you need.

[WouterDeCoster]

My guess would that those reads are DNA contamination in your cDNA library.