Hi Jiwen,
The short answer is that if your data is not pairing, then there may be
a quality problem. Or, there may be a problem with the TopHat mapping
run. The best advice is to take a sample of your data and experiment
with some TopHat alternate parameters (using the protocol suggestions in
Hi all,
After mapping, I used IGV to have a look at the mapping. There are a lot of
mapped reads without pair reads. Should I keep these reads? or Is this a
problem for cufflinks analysis?
What I tried is:
1. BAM to SAM
2. Filter SAM: set Read mapped in a proper pair to Yes.
The result is tha
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