remove illumina low quality reads

[StephaniePi83]

I have to analyse 36 nt long illumina reads.
I use bowtie for 3' end stripping (option -3 <int> ) and then i was wondering if i have to filter reads based on quality ? for example put a threshold and remove reads in wich mean quality value < threshold ... is it possible to do that with bowtie ? if no, how can i do this ?

[GenoMax]

It is always a good idea to do some QC on your reads before doing alignments.

FastQC is an excellent option (http://www.bioinformatics.babraham.a...ojects/fastqc/). You can also use the Fastx toolkit (http://hannonlab.cshl.edu/fastx_toolkit/).