Question: studying a locus for different variants of an expressed lnc-RNA
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3.1 years ago by
english.server0 wrote:

I have done FASTQ groomer, Tophat and cufflinks on FASTQ data. Now, I want to study a pre-defined strech of a certain chromosome (or a locus) for different expressed variants of a non-coding RNA. What should I do?

variants non-coding rna • 600 views
ADD COMMENTlink modified 3.1 years ago by Jennifer Hillman Jackson25k • written 3.1 years ago by english.server0
gravatar for Jennifer Hillman Jackson
3.1 years ago by
United States
Jennifer Hillman Jackson25k wrote:


Before running Cuffdiff, the Tophat results can be filtered down to the region of interest with the tool:

BEDTools > Intersect BAM alignments with intervals in another files

If you have reference annotation for the non-coding RNA sequences, these can be combined with the Cufflinks output using CuffMerge, then that result GTF used with Cuffdiff. 

Best, Jen, Galaxy team


ADD COMMENTlink written 3.1 years ago by Jennifer Hillman Jackson25k

Thank you indeed very much.

ADD REPLYlink written 3.1 years ago by english.server0
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