Low number of reads mapped, looking for a relaxed paired-end Illumina mapper

Question

[biotech]

Hi,

I mapped 2x75 Illumina to a bacterial genome using BWA with default settings. Very low number of reads were mapped. I was used to TMAP tool when worked with IonTorrent data, with high number of mapping reads always.

I'm looking for a relaxed mapping tool. Maybe could be useful to relax BWA thresholds before?

Thanks for your help,

Bernardo

Answer 1

[dariober]

You put rna-seq among your tags. Are you aligning RNA-Seq data with bwa? If so, this could partially explain your low mapping rate and I would try a splice-aware aligner like tophat. Otherwise, bwa mem might be an option to consider if you expect gaps.

[biotech]

I'm doing some checks and will update the post soon.

[biotech]

Seems the problem is not the aligner. I have very low number of RNA-seq data from the organism I'm mapping to, only 10%.

[Ashutosh Pandey]

You are studying bacteria so splice aware aligner may not be really necessary.