Hi everyone.

My name is Donny, bioinformatician from Malaysia.

Currently I am using Cuffdiff, trying to explore the differentially expressed genes within a sets of data (without replicates). There are a total of 6 condition overall and I would like to seek for some advice here with the Cuffdiff command lines. Thank you very much for that! =)

I understand that if we were comparing 2 conditions, the command line would be something like:-

$ 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

This command line was based on the TopHat paper.

Note: C denotes for sample, while R denotes for replicates.

What if I have 6 conditions (without replicates)?

Should the command line be something like:-

$ cuffdiff -o diff_out -b genome.fa -p 8 -L C1,C2,C3,C4,C5,C6 -u merged_asm/merged.gtf \
./C1_thout/accepted_hits.bam, ./C2_thout/accepted_hits.bam, ./C3_thout/accepted_hits.bam \
./C4_thout/accepted_hits.bam, ./C5_thout/accepted_hits.bam, ./C6_thout/accepted_hits.bam

Later on, I hoped to be able to compare the groups like C1 vs C3 or C4 vs C6 etc..

Thank you very much in advance!