Problems with cuffdiff

Question

[hothriananya]

Hi,

I have been using the below cuffdiff code to compare my samples and find DEG's, I dont know why cuffdiff is not taking labelling part

cuffdiff -p 5 -o Diff -L WT,KO merged_asm/merged.gtf WT1/WT1_accepted_hits.bam WT2/WT2_accepted_hits.bam,KO1/KO1_accepted_hits.bam KO2/KO2_accepted_hits.bam

It returns with the error

Error: number of labels must match number of conditions

Can anyone help me on this error please, Thanks in advance.

Answer 1

[Devon Ryan]

The error is saying exactly what the problem is. It's likely that you meant to use this:

cuffdiff -p 5 -o Diff -L WT,KO merged_asm/merged.gtf WT1/WT1_accepted_hits.bam,WT2/WT2_accepted_hits.bam KO1/KO1_accepted_hits.bam,KO2/KO2_accepted_hits.bam