I have somehow naive questions.
I have two conditions which I would like to compare. In each condition, we have three replicates.
When, I try to do the cuffmerge command (based on nature protocol paper, 2012,
assemblies.txt file say that
but I think that the bold line should be changed as follows.. Is it right? (I am not sure)
(since current Corrigendum doesn't mention about it, I am wondering whether I am right or not..)
Also, cuffdiff command,
cuffdiff -o diff_out -b genome.fa -p 8 –L C1,C2 -u merged_asm/merged.gtf \ ./C1_R1_thout/accepted_hits.bam,./C1_R2_thout/accepted_hits.bam,./C1_R3_thout/ accepted_hits.bam \ ./C2_R1_thout/accepted_hits.bam,./C2_R3_thout/accepted_hits.bam,./C2_R2_thout/ accepted_hits.bam
also changed as
cuffdiff -o diff_out -b genome.fa -p 8 –L C1,C2 -u merged_asm/merged.gtf \ ./C1_R1_thout/accepted_hits.bam,./C1_R2_thout/accepted_hits.bam,./C1_R3_thout/ accepted_hits.bam \ ./C2_R1_thout/accepted_hits.bam,./C2_R2_thout/accepted_hits.bam,./C2_R3_thout/ accepted_hits.bam
Is it right? OR I am missing something?
I realized that the order of gtf file in assemblies.txt makes difference in cuffmerge result.
So, I want to make sure I am right..
Thanks in advance