Does the order of trimming reads first and then filterings or first filtering reads and then trimming make a diffrence?
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I did trimming of bad quality bases first. I think you can retain more of your reads like this, because after that step more of your reads will pass the filtering step.
Maybe you could try both ways with a subset of reads and see which one yields more reads after filtering.
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Not sure myself. Generally, I've done
Filtering of contaminant genomes (YMMV), then Trimmomatic with the appropriate adaptors. For Trimmomatic, I'm not quite sure if they trim adaptors first then do quality trim, or vice versa.
That said...what did you mean by filtering?Last edited by ctseto; 10-29-2013, 05:41 AM.
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Originally posted by Seraphya View PostThe subset test is a good idea.
I am actually wondering what the purpose of filtering is if you are trimming reads down and discard them when there are not enough bases left.
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It depends on what you want to do with your reads. For mappings I wouldn't filter too strictly. For assemblies you want the best quality reads possible.
In the case of an assembly I remove reads with ambiguous bases first. Assemblers don't handle them well. Then you trimm and then you filter. I try to estimate how many reads I need in the end for a decent assembly. There are some numbers here in the forum for a few species. Then I iterate the filter criteria with a subset in a way to approximately reach that number.
The more reads you have to begin with the more you can filter out resulting in higher quality of the remaining.
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