Hi,
I have two paired-end sequencing RNA-Seq libraries. Both of them are from the same sample but prepared using different insert lengths. I've run tophat on both of them separately. Now I want to run Cufflinks. I was wondering if it is a good idea to merge tophat accepted_hits.bam files for different insert lengths and run Cuffllinks on the merge file?
My goal is to detect splice variants for the whole sample.
Thanks
I have two paired-end sequencing RNA-Seq libraries. Both of them are from the same sample but prepared using different insert lengths. I've run tophat on both of them separately. Now I want to run Cufflinks. I was wondering if it is a good idea to merge tophat accepted_hits.bam files for different insert lengths and run Cuffllinks on the merge file?
My goal is to detect splice variants for the whole sample.
Thanks
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