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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