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Old 04-11-2012, 08:21 AM   #1
Location: France

Join Date: Sep 2011
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Default remove illumina low quality reads

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 ?
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Old 04-12-2012, 04:12 AM   #2
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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 (
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