Question: Fastq-Mcf
gravatar for Benoît REMENANT
6.7 years ago by
Benoît REMENANT10 wrote:
Hi all, Does someone know fastq-MCF? We are relatively newbies in analysing RNAseq results, and we would like to use the fastq-MCF program to trim our illumina sequences (based on quality score and adapters sequences) while keeping paired reads synchronized. Unfortunately, there are some parameters we did not understand, like -s (log scale for clip pct to threshold) and -t (% occurrence threshold before clipping). Does anyone can explain us what these parameters mean? Or when I can found useful information? And do you think we have to unable the PF filtering (and why)? Thank you very much in advance if someone can help us. Benoit
ADD COMMENTlink modified 6.7 years ago by Jennifer Hillman Jackson25k • written 6.7 years ago by Benoît REMENANT10
gravatar for Jennifer Hillman Jackson
6.7 years ago by
United States
Jennifer Hillman Jackson25k wrote:
Hi Benoit, The best person to ask about parameters is probably the tool author. The wiki source has some comments, but not in the detail you are looking for: It looks like the author is answering questions at A search on "fastq-mcf" found four threads, the largest one with quite a but of parameter clarification in it. This would be a good place to post a new question question about any parameters not covered in the other threads. Hopefully this helps, Best, Jen Galaxy team
ADD COMMENTlink written 6.7 years ago by Jennifer Hillman Jackson25k
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