Help for Fastx_clipper

[superqqq]

I am a newbie to this forum. I currently use FastQC and fastx for my RNA-seq data cleaning (75bp paired end).

From FastQC, I got some over-represented sequence (0.1-1% OPS). Some of them are annotated as Truseq adapters or PCR primers, so I treat them as adapter and try to remove them from my raw dataset. When I use fastx_clipper -a OPS, it seems trimmed more then I expected. So does it mean it allow mismatch or some sequence contain part of the OPS are also get trimmed, and leaves me a lot of short reads and FastQC reports become worse. Anyone have similar experience and could you share with me the cretiera you used for this clipper command?

By the way, anyone know where to find the fastx source code? It seems not on the website.

Thanks very much for your time and effort!

[sammy07]

Hi, have a look at this thread: http://seqanswers.com/forums/showthread.php?t=16056

Might be that fastx_clipper doesn't always do what you expect; you might have to validate the output or to use cutadapt instead.