How to analyze Cufflinks data

Question

[rydharri]

I apologize for the obviously broad and possibly dumb question. I have an Excel sheet made using Cufflinks showing alternative splicing quantification from an original RNA-Seq.

I don't know much more to say about this, other than the fact that I am sure there is an easier and more efficient way to try and find possible alternative splicing events than manually going through all 8 spreadsheets containing tens of thousands of genes each?

The only tool I have come across is Enrichr, though here I do not know how exactly I should choose my genes for analysis.

Any help is appreciated. And again I am sorry I am not a programmer obviously :(

Answer 1

[Satyajeet Khare]

Cufflinks assembles transcripts using aligned RNA sequencing reads and produces gtf file as an output. In an ideal scenario, one will merge all such gtf files into one single merged gtf file using cuffmerge. cuffdiff will then be used for normalization and analysis of differentially expressed and processed genes.

For use of subsequent tools, you will need to know more details about these cufflinks files such as genome assembly and versions used for alignment. And even before that, you may want to confirm that the files are indeed in gtf format.

Considering FPKM values directly from cufflinks without normalization may lead to errors.