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I've been using Illumina data but the data which I got contain a lot of low quality data.
I tried to set a variety of trimming using quality score. If I set too strict, 70 or 80% of reads are trimmed. Also some reads are very short after trimming, for example, only 5 bp - So I need to set some threshold regarding the length of reads I want to remain.
I'll use this data for RNA-seq so reads should be relatively accurate, I imagine.
I'm wondering how people decide or justify how much quality trimming is good enough.
I guess that not only one solution but I'd like to hear comments.
Thanks!
Jasmine
I tried to set a variety of trimming using quality score. If I set too strict, 70 or 80% of reads are trimmed. Also some reads are very short after trimming, for example, only 5 bp - So I need to set some threshold regarding the length of reads I want to remain.
I'll use this data for RNA-seq so reads should be relatively accurate, I imagine.
I'm wondering how people decide or justify how much quality trimming is good enough.
I guess that not only one solution but I'd like to hear comments.
Thanks!
Jasmine