Problem with bad quality bases in RNAseq
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Hi silas008, as a rule of thumb, you should be doing quality trimming (i.e., fastq_quality_trimmer) then adapter clipping (fastx_clipper) before mapping small RNA reads.
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What is your read length? If it is long then you would cut the ends anyway.
Reads = 36nt. Shoul I cut the ends to obtain reads 18-30nt?
Well if your reads are 36nt and 30 bases out of that are bad it will be a challenge to get useful information out regardless what you do.
I think he means base 27 onwards are bad quality. And yes, if they are bad quality you should trim, but if base 26 is good why did you trim it?
I see, I misread that section. There is no problem them ;-)
Sorry. The bad quality scores are about 27 base, not exactly 27. But before 25 base I have very good quality scores.