I am trying to run Cuffdiff to conduct a differential expression analysis. I am running the following command (I am using two data sets as a sample, one from each experimental group, until I can get it to run correctly):
cuffdiff c:/research/Cuffmerge/merged_asm/merged.gtf c:/research/alignment_data/TB1_alignment_sorted.sam c:/research/alignment_data/NT1_alignment_sorted.sam
I keep on receiving empty output files either with or without an error message (depending on small changes I make to the script). I tried troubleshooting quite a bit- I am running the command with different arguments and also made sure that the transcripts were properly labeled with tss_id and p_id.
I broke up the command to try to find the problem:
I first ran it without any labels. The output is a set of empty files and the following command line message:
You are using Cufflinks v2.2.1, which is the most recent release.
Then I ran the script without the paths and got this error message:
You are using Cufflinks v2.2.1, which is the most recent release. open: No such file or directory Error: cannot open file TB1_alignment_sorted.sam for reading. Unrecognized file type
Some outputs also make it seem like the second file isn't being detected:
cuffdiff requires at least 2 SAM files
The return value on these commands is 0- so I don't know why they aren't being executed properly.
What is going wrong?