No unmapped reads... is that common?

[Adam Cornwell]

Working with a few mouse samples, I've used STAR to generate a few different genomes and have performed alignments to each of them. Each sample has 20-30 million reads. I'm almost surprised that for each of the three genomes, there appears to be not a single unmapped read for any sample, according to SamStat (which I ran on the bam files I made from STAR's sam files). Is that... common? Low quality reads were filtered out prior to the fastqs being fed into STAR, but I still would have expected some kind of artifact to be in there somewhere and end up not aligning. Since this is my first time through this process, I just want to make sure this isn't something unexpected.

Thanks again,
Adam

[Nicolas Robine]

Which command did you use? I willing to bet that the unmapped reads are incorporated in the SAM files and that SamStat don't pick them up because of discrepancies in the SAM format (output by STAR on one side, read by SamStat on the other side).

Did you look at the Log.final.out file?

Nicolas

--
Nicolas Robine, PhD

Bioinformatics Scientist, NYGC
nro...@nygenome.org 

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[James Blachly]

STAR default is NOT to output unmapped reads, so the output SAM would therefore consist only of mapped reads (i.e. stats would tell you 100% mapping rate)

[Varun Gupta]

Hi
You can use --outSAMunmapped Within  and you will get unmapped reads within Alignment.out.sam.

By default STAR only outputs mapped reads.

Hope this helps

Varun

[Adam Cornwell]

That would certainly do it. I was using the full SAM output mode, but didn't use the option for including unmapped reads. Thanks for the heads up on the log.final.out- I really like the verbosity of the STAR output (including log.out) but there's enough info in there that I didn't get a chance to look all the way through them before. Thanks for the help.

On Thursday, August 1, 2013 4:28:34 PM UTC-4, Adam Cornwell wrote: