cuffcompare error: cannot locate input file

Question

[catherine]

I used tophat to map, and cufflinks to get gtf file with and without reference file. Now I what to compare these two gtf files by using cuffcompare, but I keep getting error when run cuffcompare.

Many thanks in advance for any idea.

My command is

cuffcompare -i withGTF/transcripts.gtf withoutGTF/transcripts.gtf -o Compare/

And my error is

Error: cannot locate input file: Chr1    Cufflinks    transcript    3631    5899    1000    +    .    gene_id "AT1G01010"; transcript_id "AT1G01010.1"; FPKM "7.2820387528"; frac "1.000000"; conf_lo "6.676099"; conf_hi "7.887978"; cov "20.013303";

Answer 1

[Vivek]

The -i option in command line needs to be a text file containing a list of GTF files, not the GTFs themselves. From the help:

-i provide a text file with a list of Cufflinks GTF files to process instead
of expecting them as command line arguments (useful when a large number
of GTF files should be processed)