[help] Cuffdiff with BAM or SAM files

[stavi]

Hello everyone!

I am new here in this forum, I hope it is okay if I start with asking stupid questions about "Cuffdiff".

With TopHat and Cufflinks I got some "sorted.bam" and "accepted_hits.bam" files of 2 different probes, to go on and design some nice graphes, but I got a problem with starting Cuffdiff.

So here is my problem:

1. I run TopHat and Cufflinks with my probes and get for each a file called "transcripts.gtf"

2. I created a file called "assemblies.txt" with the pathway for the transcripts.gtf for my 2 probes

3. runned cuffmerge
cuffmerge -g /pathway/xy.gtf /pathway/gen.fa assemblies.txt

4. tryed out ciffdiff command with the merged gtf

cuffdiff -o diffProbes -b /pathway/gen.fa -L Probe1.sam Probe2.sam -u /pathway/merged.gtf

But I got Error:

At least 2 SAM files needed... but the 2 SAM files are in this folder. So I tryed the same with BAM files, it doesnt work either. It should work... but it doesnt.

can someone help me? thanks a lot!

Stavi

[dpryan]

You're telling cuffdiff that the Probe1.sam file is to be used for labels. It's really unlikely that that's what you want to do.

BTW, you're best off sticking to the syntax described on the cufflinks webpage.

[stavi]

I think I got it now, Cuffdiff is working now since 4 hours. Thanks.