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-   -   the low percentage of mapped reads (http://seqanswers.com/forums/showthread.php?t=18936)

wangli 04-03-2012 07:49 PM

the low percentage of mapped reads
 
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 04-03-2012 11:31 PM

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 04-04-2012 05:56 AM

Got it, Thanks a lot!


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