Cufflinks Question: how to find assembled parts differing from annotated parts?

Question

[biolab]

Dear all

I am new using tophat2 and cufflinks. To my knowledge, one function of cufflinks is to assemble mapped reads into longer parts based on annotation file. I need to find new assembled transcripts that differ from the annotated transcripts or brand new transcripts not been collected in annotation file.

Cufflinks has four output files, among which the transcripts.gtf file seems to be what I am looking for. But I don't know how to achieve my goal. Wish you provide me some advice. THANK you very much!

Answer 1

[GouthamAtla]

If you do not provide the GTF file, it will de-novo assemble transcripts and generates a GTF file and this file can be compared with standard GTF file. If you are looking for specific genes, subset the bam file only at regions of interest and run cufflinks.

[biolab]

Hi Geeky, your answer is helpful, thanks a lot!