Hello,
I recently mapped 8 RNA-Seq samples using STAR. The samples are paired. The data in log.final.out for each sample look very similar to the sample's partner - with one exception.
I have one sample that shows 6.57% reads mapped to multiple loci and 32.38 % of reads unmapped: too short. It's partner shows 24.30% and 13.12%, respectively (these numbers more closely resemble the other samples). Uniquely mapped reads: roughly 60% for both.
I am wondering why the first sample has such a high percentage of "unmapped:too short" reads. I've read that sequencing quality can affect this number, so I expected the the sample to be low quality. However, Fastqc shows that the sequencing length and base quality is very good (and similar) for both samples. Can anyone help me to explain this?
Thanks for your help in advance!
I recently mapped 8 RNA-Seq samples using STAR. The samples are paired. The data in log.final.out for each sample look very similar to the sample's partner - with one exception.
I have one sample that shows 6.57% reads mapped to multiple loci and 32.38 % of reads unmapped: too short. It's partner shows 24.30% and 13.12%, respectively (these numbers more closely resemble the other samples). Uniquely mapped reads: roughly 60% for both.
I am wondering why the first sample has such a high percentage of "unmapped:too short" reads. I've read that sequencing quality can affect this number, so I expected the the sample to be low quality. However, Fastqc shows that the sequencing length and base quality is very good (and similar) for both samples. Can anyone help me to explain this?
Thanks for your help in advance!
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