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 On 3/2/12 12:25 PM, Benoît REMENANT 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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