Hi, I am analyzing paired-end reads (Illumina) and I want to use qiime quality-filter q-score-joined. In the interactive quality plot description, the minimum sequence length identified during subsampling bases was 240 bases in forward and 80 bases in reverse sequencing, is it the variation are not at all problem with further quality trimming? or anything i have to consider at here?
In general, QIIME2 recommend setting this value to a length where the median quality score begins to drop below 30, or 20 if the overall run quality is too low.
In my run i got median quality score begins at 37 and drp at 32 for forward sequences, for reverse sequences it is different score shows that is the highest is 38 and least is 24 only at the position 251 quality score is 18 only. How can I set the trim length (p-trim-length) and how to use the job position (p-jobs-to-start) in deblur denoise. Here i pasted the interactive quality plot results for your kind reference.
Good evening Srinivasan,
It tells us that some sort of trimming has already taken place. (Illumina reads are always all the same length directly off the instrument.)
As of now, deblur only uses the forward read. So in this specific case, you don't have to worry about your strange reverse read at all!
If you do want to use both reads, you could first join them using vsearch join-pairs, then process them with deblur. This may require trimming to join well, but you will have to try it and see.
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