Having problem running cuflinks v2.2.1 output
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
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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)?
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?
You might just be able to grep for those codes, I'm not sure. In any case, you have the right idea!
You had asked similar kind of question here, I had replied, see if its useful for you.
Thank you so much for sharing the information. I will try it.