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Forum: RNA Sequencing 05-24-2016, 11:24 AM
Replies: 6
Views: 3,476
Posted By ivygreen
Hi Michael Ante, I'm pretty new to these...

Hi Michael Ante,
I'm pretty new to these programs. I ran cufflinks on a few samples - how do I interpret the resulting reports? Also, if the files are indexed with different alignments (which I now...
Forum: RNA Sequencing 01-26-2016, 06:24 PM
Replies: 6
Views: 3,476
Posted By ivygreen
I tried re-running without the -u option, but all...

I tried re-running without the -u option, but all FPKM are still 0.
Forum: RNA Sequencing 01-26-2016, 09:03 AM
Replies: 6
Views: 3,476
Posted By ivygreen
Reads Mapped but 0 FPKM for Every Gene

Hi all,

I'm using Tophat 2.1.0 and Cufflinks 2.2.1 to analyze mouse RNA sequencing. I used Tophat to align the reads, and this step appeared to be successful. A sample alignment summary for one of...
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