Question: running Tophat on merged reads
gravatar for rob.costa1234
4.2 years ago by
United States
rob.costa1234250 wrote:

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

rna-seq merged reads • 919 views
ADD COMMENTlink written 4.2 years ago by rob.costa1234250

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.

ADD REPLYlink written 4.2 years ago by genomax87k

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.

ADD REPLYlink modified 4.2 years ago • written 4.2 years ago by igor11k
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