Question: Cuffdiff analysis output
gravatar for Wanderer
9 months ago by
Wanderer10 wrote:

Hi there,

I tried to run cuffdiff with the annotation of iGenome but still no sucess to have a output with all statistics results, some results on cuffdiff output are empty

@jen any news about the fix of this tool? is there any alternative to cuffdiff working?

Thank you!

rna-seq cufflinks cuffdiff • 395 views
ADD COMMENTlink modified 9 months ago • written 9 months ago by Wanderer10
gravatar for Jennifer Hillman Jackson
9 months ago by
United States
Jennifer Hillman Jackson25k wrote:

As far as I know, Cuffdiff was not impacted. The tool would (should!) fail if the problems are related to the conda fixes occurring at Galaxy Main right now, not produce incomplete results.

Do you have an example line or two from the Cuffdiff output that presents with missing statistics? Is that record in the iGenomes GTF complete (contains p_id, tss_id, and gene_name)? You can post back both in a comment if you would like feedback.

Or are some output files completely empty? That would mean that more is going on. Let us know and we can look at your history if working at

ADD COMMENTlink written 9 months ago by Jennifer Hillman Jackson25k

I did the cuffcompare run before running cuffdiff to put p_id and tss_id, the annotation has gene_name, look the output:

SQLite Database CDS [30796] CDSCount [61592] CDSData [61592] CDSDiffData [19729] CDSExpDiffData [30796] CDSFeatures [0] CDSReplicateData [61592] TSS [28379] TSSCount [56758] TSSData [56758] TSSExpDiffData [28379] TSSFeatures [0] TSSReplicateData [56758] attributes [0] biasData [0] features [0] geneCount [48020] geneData [48020] geneExpDiffData [24010] geneFeatures [0] geneReplicateData [48020] genes [24010] isoformCount [81498] isoformData [81498] isoformExpDiffData [40749] isoformFeatures [0] isoformReplicateData [81498] isoforms [40749] model_transcripts [0] phenoData [0] promoterDiffData [24010] replicates [2] runInfo [4] samples [2] splicingDiffData [28379] sqlite_sequence [0] varModel [41824]

ADD REPLYlink written 9 months ago by Wanderer10

If you are using the iGenomes annotation, then running Cuffmerge to create the input GTF for Cuffdiff is how to incorporate novel isoforms and generate full statistics. Specifically, input your Cufflinks GTFs + iGenomes GTF to Cuffmerge. This will produce a proper GTF to use with Cuffdiff for discovery. Use the iGenomes GTF directly for knowns.

ADD REPLYlink written 9 months ago by Jennifer Hillman Jackson25k

Thank you Jen!! Now I am trying another methodology because cummeRbund isnt working yet, anyway thanks!!

ADD REPLYlink written 9 months ago by Wanderer10
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