SQLite file from Galaxy gives "0 obs."

Question: SQLite file from Galaxy gives "0 obs."

12 months ago by

eculfa • 10

Turkey/Istanbul/Üsküdar American Academy

eculfa • 10 wrote:

Hello!

After I have performed Cuffdiff in Galaxy on my two RNA-Seq data of different treatment conditions, I loaded my SQLite data into RStudio to see the differentially expressed genes. However, after I command; "gene_diff_data <- diffData(genes(cuff_data))" I don't see any data available in R. The only available info in R is "0 obs. in 11 variables". What could be the reason for this? Where have I done wrong? My galaxy run progressed pretty smoothly.

Thank you! Efraim

rna-seq sqlite R • 387 views

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modified 12 months ago • written 12 months ago by eculfa • 10

12 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

You probably need to initialize the cuff_data object first:

cuff_data<-readCufflinks()

or skip the underscore and keep the name simple to use in downstream functions:

cuff<-readCufflinks()

Reference: http://compbio.mit.edu/cummeRbund/manual_2_0.html

Hope that helps! Jen, Galaxy team

ADD COMMENT • link modified 12 months ago • written 12 months ago by Jennifer Hillman Jackson ♦ 25k

12 months ago by

eculfa • 10

Turkey/Istanbul/Üsküdar American Academy

eculfa • 10 wrote:

hi! I have followed the instructions that you gave but it still wouldn't work. In the meantime, I have googled to see if others had experienced similar problems to find there doesn't seem to be a step by step troubleshooting of the problem. Later on, I tried to get my figures in galaxy but it was to no avail. I got this error after I tried to run cummeRbund on galaxy; "Attempting to run a tool with empty command definition." I later on read that it might be a bug ; https://github.com/galaxyproject/tools-devteam/issues/340 Since I had failed on both platforms, could it be due to one of the galaxy tools I used during my processing of data?

Thank you so much for the quick feedbacks! I truly appreciate Galaxy Team's effort! Efraim

ADD COMMENT • link written 12 months ago by eculfa • 10

Yes, graphing this data is not possible until the fix. The ticket you are following will be updated and closed once done. Thanks, Jen, Galaxy team

ADD REPLY • link written 12 months ago by Jennifer Hillman Jackson ♦ 25k

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