why low mapping rates for RNAseq?

[[email protected]]

The bioinformatic person is doing all that. She trimmed the adapters and tried aligning the reads to the genome using tophat. She got 40% alignment there. We tried blasting some of the unaligned reads and realized that something went wrong with the tophat run as some of them were aligning to chromosome M, chr 1, 4 etc. She will be doing the alignment again with STAR this time but to save on time she also ran the RSEM along side and got these low percentage alignments to transcriptome so I wanted to know if we are missing out on anything?

[Brian Bushnell]

It would be helpful if you posted some basic quality metrics, such as you get from FastQC. There's not enough information to determine what the problem is or even if there is a problem.

[[email protected]]

Ok. I have looked at the FastQC report of the samples and it looks fine to me. What kind of information should I give from FastQC report?

[Brian Bushnell]

The whole thing as PDF is good way to start. But particularly the quality histograms, anything that failed the tests, and anything related to mapping. And the stats from adapter trimming, the command lines you used for each program, the top hits and mapping rate you got from Blast... etc.

[[email protected]]

I will have to ask my bioinformatician for the stats after adapter trimming. I will get back on this. Thanks for your time.