Having problem running cuflinks v2.2.1 output

Question

[hana]

I am having trouble getting Cufflinks v2.2.1. output. I have run cufflinks with reference annotation file and got the reasonable results. In order to find the potential novel isoform, I run cufflinks without any reference annotation file but cufflinks output only contained the information of chr1 and the transcript.gtf file is not readable.

I am wondering if anybody met the same problem before and what is the solution?

Thanks in advance

[Devon Ryan]

Why not give cufflinks the GTF file and use the -g rather than -G option (actually, I'm not sure -G is even an option in the most recent versions)?

[hana]

Thank you for your reply . If I use cufflinks with -g option then can I run cuffcompare on transcript.gtf output file in order to find the number of codes "x" , "i" , "u"and "j" in my output result?

[Manvendra Singh]

You had asked similar kind of question here, I had replied, see if its useful for you.

[hana]

Thank you so much for sharing the information. I will try it.

[Devon Ryan]

You might just be able to grep for those codes, I'm not sure. In any case, you have the right idea!