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Old 02-06-2014, 08:07 PM   #4
natar210@gmail.com
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Location: Melbourne

Join Date: Jun 2013
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On this note ..I Have a question. I am doing PE RNA-Seq analysis of mouse data. My read length is 90bp and fragment size is 127 bp which means I have overlapping reads. I used Flash and found that not all reads overlap.

I have a file with merged reads which overlaps and also two files with non overlap reads. basically three fastq files.

How do I go about running Tophat with this and I am not really sure hot to calculate the mean inner mate distance and sd??

Has anyone come across this situation???
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