the low percentage of mapped reads

[wangli]

Hi all

I am analyzing RNA-seqs of poplar species generated by Illumia Hi-Seq with the CLC genomic workbench.
I set the minimum length fraction as 0,7 and minimum similarity fraction as 0,6, Maximum number of hits for a read as 10.
The mapped reads only take around 70% among all reads.
Is this percentage too low? Any idea to improve that? BTW, they are paired-end 100 bp reads.

Thanks!

[kopi-o]

It sounds OK. The mapping percentage will depend on various things such as read quality, the quality of the reference genome assembly, and properties of the genome itself (repeats, pseudogenes etc).

[wangli]

Got it, Thanks a lot!