Trimming with R and bioconductor

[Romz34]

Hi,

I'm trying to trim RNAseq with a bad quality score with bioconductor. My main problem is that the sequenes are paired-end and I want to keep "orphan" sequences generated by the trim in another files.
I know that some programs like Trimmomatic do that automaticly. I wonder if something like that exist in R. Wh

at I find are functions from Biostring (trimLRPattern) and ShortRead. They are usefull for delete patterns and adapter, but can't find functions for delete entire sequences, keeping the paired-end.

Thanks.
Romain.

[Romz34]

Finally I did a little script to do that. Here is the script :

http://pastebin.com/Jqss1kPc

(optimised by waqueteu)

For this example, I choose quality mean > 20, but you can change it if you want.
Thanks,
Romain.