Question: cuffdiff error "number of labels must match number of conditions"
gravatar for Bioiris
3.4 years ago by
Bioiris0 wrote:

Hello, I use cuffdiff qualification of 20 .bam files

in my snakemake, I have

cuffdiff rule:

     input: bam = expand ( "output / bam / smp {} .bam" smp = config ["samples"] split ().)

     output: "output / cuffdiff / done"

     params: gtf = config [ "gtf"], args = config [ "cuffdiff"] [ "args"] = labels config ["samples"] split ().

     Threads: config [ "cuffdiff"] [ "threads"]

     message: "" "--- cuffdiff contifiquation." ""

     shell: """

 cuffdiff -p {threads} -o {output} -L  {input.bam} {params.gtf} {input.bam}

 touch {output} """

but, i have this error

"" "You are using Cufflinks v2.2.1, qui est The Most recent release.

Error: number of labels must match number of conditions' ""

can anyone help me ??

thank you in advance

rna-seq • 3.0k views
ADD COMMENTlink modified 2.1 years ago by Biostar ♦♦ 20 • written 3.4 years ago by Bioiris0

See this error in cuffdiff ---(mutiple sample comparision) for how to specify labels for the conditions being compared. If you have only one condition (control, test) then there will be two labels.

ADD REPLYlink modified 3.4 years ago • written 3.4 years ago by genomax75k

Please post the actual command used.

ADD REPLYlink written 3.4 years ago by igor8.9k

Previously I also faced this problem and a solution given in this thread by Devon Ryan solved it.

ADD REPLYlink modified 2.1 years ago • written 2.1 years ago by rice.researcher140
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