Dear Noa,
I also feel the same. So I think it would be better to use these three steps
remove sequencing artifacts
then trim the sequences by from the 5' end or if needed from the 3'end also (2-5 bases, depending on your sequence quality)
finally filter the sequences by quality (I used the default parameters). Although it removed 15% of the sequences but I feel confident with the high quality data.
Any better suggestion will be appreciated.
CHeers,
Bomba
On Thu, Mar 1, 2012 at 10:48 AM, Noa Sher noa.sher@gmail.com wrote:
Hi
I am looking at various options of quality trimming sequences for RNA Seq analysis
I know I can chop off a certain number of bases off the 3' or 5' ends of the reads.
Is it possible to use a sliding window to chop reads to different lengths, leaving everything above quality score 20 (for example) or would this be inadvisable as the differing lengths of reads would skew the downstream FPKM analysis?
Thanks
noa
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