running Tophat on merged reads

Question

[rob.costa1234]

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

[GenoMax]

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.

[igor]

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.