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?
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