Question: Fastq-Mcf
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gravatar for Benoît REMENANT
6.6 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
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ADD COMMENTlink modified 6.5 years ago by Jennifer Hillman Jackson25k • written 6.6 years ago by Benoît REMENANT10
0
gravatar for Jennifer Hillman Jackson
6.5 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: http://code.google.com/p/ea-utils/wiki/FastqMcf It looks like the author is answering questions at http://seqanswers.com. 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 6.5 years ago by Jennifer Hillman Jackson25k
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