running Tophat on merged reads
I ma merging the forward and reverse reads using Seqprep. Now when I run TopHat should I be using single end option in that there is only one Fastq. I think PE information is already merged. Any pointers
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rob.costa1234
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What pointers do you need beyond what you have written above? Now the reads would be single-end but longer than the original length. Kind of odd that you have reads for RNAseq that are actually overlapping, the inserts must be (relatively) short.
Why are you merging your reads? That's only needed in very specific circumstances. If you are using TopHat, you don't need to do that.