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 ?
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 ?
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