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
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
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