My RNA-seq data is non-stranded. How can I use Cufflinks?

Question

[heniswydryn]

My RNA-seq data is non-stranded. I've used a TopHat Analysis and now I wanted to proceed to Cufflinks. There is a box to select whether our data is stranded and obviously, I don't select it. But if I don't, I'm not allowed to proceed with the analysis. It says only TopHat alignments that match the strandedness will show up to be selected for further analysis. Have you ever encounter this problem? Can you help me?

Thanks in advance!

[heniswydryn]

I'm following that exact paper, actually! =)

It's not exactly an error. There's this box saying "Stranded", which I leave empty. But then I cannot choose any samples to proceed with the Cufflinks analysis. However, if I tick that box, all samples are immediately in the panel to be selected.

Answer 1

[GouthamAtla]

Most of the times, rna-seq data is not stranded. The tuxedo pipeline should work fine with non-stranded data. What is the exact error/warning/message that you get?

And what is that 'Box'? Are you using any GUI tool that wraps tuxedo pipeline?

[heniswydryn]

Maybe I should add that I'm using the BaseSpace platform...