Question: Low number of reads mapped, looking for a relaxed paired-end Illumina mapper
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gravatar for biotech
5.1 years ago by
biotech540
United States
biotech540 wrote:

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

rna-seq snp illumina • 1.7k views
ADD COMMENTlink modified 5.1 years ago by dariober10k • written 5.1 years ago by biotech540
0
gravatar for dariober
5.1 years ago by
dariober10k
WCIP | Glasgow | UK
dariober10k wrote:

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.

ADD COMMENTlink written 5.1 years ago by dariober10k

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

ADD REPLYlink written 5.1 years ago by biotech540

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%.

ADD REPLYlink written 5.1 years ago by biotech540

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

ADD REPLYlink written 5.1 years ago by Ashutosh Pandey11k
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