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Hi,
I am planning to run tophat on my paired-end RNA-Seq data library (75 bp length). Before running tophat, I checked the quality plots. The left end reads look fine but for the right end reads, the quality values suddenly drops after 46th base pair. I am attaching the distribution plots. I am not sure what's going on.
I am planning to trim the low quality nucleotides from right end reads.
I am wondering what parameters of tophat should I choose (--segment-length and other mismatch values)?
Any idea plz.
Plots http://www.mcdonaldlab.biology.gatec...fastq.qual.pdf
I am planning to run tophat on my paired-end RNA-Seq data library (75 bp length). Before running tophat, I checked the quality plots. The left end reads look fine but for the right end reads, the quality values suddenly drops after 46th base pair. I am attaching the distribution plots. I am not sure what's going on.
I am planning to trim the low quality nucleotides from right end reads.
I am wondering what parameters of tophat should I choose (--segment-length and other mismatch values)?
Any idea plz.
Plots http://www.mcdonaldlab.biology.gatec...fastq.qual.pdf