Cuffdiff - Error: number of labels must match number of conditions

[Dani]

Hi,

when I tried running cuffdiff on two files (output from STAR) it would give me the XS label missing error, then I changed my command to include the library nature (see below), but then I suddenly started getting the error: number of labels must match number of conditions.
But then if I omit the library type again I get the XS tag/label missing error indicating it needs the library info...

cuffdiff -o S46diffout -b /home/dgavino/genomes/GRCh38.primary_assembly.genome.fa —-library-type fr-firststrand -p 8 -L 2pS6,2qS4 -u /mnt/users/dgavino/Alignments/merged_asm/merged.gtf ./2pS6R1Aligned.sortedByCoord.out.bam ./2qS4R1Aligned.sortedByCoord.out.bam

Any ideas?

[Brian Bushnell]

I suggest you use DESeq or edgeR, both of which seem to produce more accurate results than CuffDiff, as well as being more stable. The Tuxedo package is not very good, IMO.

[Dani]

That's what I am starting to realize...thanks! Using the output from Cufflinks though? Or does anyone have better experience with HTSeq?
Seems harder for non-programming-savvy like me, no?

[Brian Bushnell]

Cufflinks should not be necessary... just the mapped sam files.