RNA seq trimming

RNA seq trimming


I am writing to know if 2-4 percent n content near the both ends of a sequence (RNA seq, read length:150) would be a problem and need trimming?



It depends on the aligner that you use. If you’re using something like hisat2 that does end-to-end alignment, then you’ll want to run things through a trimmer pretty much regardless of how good/bad they look. If you’re using an aligner like STAR, that does local alignment, then you don’t need to both trimming (if there’s a LOT of N content or adapter contamination then you still might want to…or you could just tweak the STAR settings). My general suggestion would then be to use STAR and not usually have to worry about trimming.

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