I am using NextGenMap to map RNAseq reads of length 100-300 bp. Obviously, many reads span multiple exons. However, I am unable to find parameters to correctly align reads mapping to spliced regions.
I tried multiple values for read-gap-penalty, gap-extension penalty and mismatch penalty, and I am using affine gap penalty function, however with no success. I start to think that NextGenMap simply cannot do it properly, which I find hard to believe. I attached a snapshot of the same set of reads mapped with NexGenMap (bottom tracks) and BBmap (top 2 tracks).
As you can see, BBmap is performing much better, opening gaps in the reads across introns, as expected.
Maybe someone could give me tips on how to adjust alignment parameters in NextGenMap to achieve correct mapping?
Remark 1: I need to use NextGenMap, as BBmap is not spitting out Bam file tags I need for downstream analysis.
Remark 2: I need to get as much coverage as possible from each read. Unambiguous mapping to a position is not enough.