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• quantity of each replicate / id conversion
  Hi I need an information about the quantity of genes in each replicates how to do it I am using ...
• converty cuff id to gene id
  Hi, wondering if anyone could give me some clues how to convert cuff gene id to normal gene id so...
• Get Gene Name From Cuffdiff'S Output?
  Hi guys, I am trying to examine gene differential expression in my mouse samples using : Cufflink...
• Cufflinks analysis remains in que without running
  Hi Team, Loving Galaxy! When I run my data, I use the same protocol for most all datasets. Howev...
• How to get counts for transcripts for all replicates
  Hi BIOSTARS, I have lots of samples that have been aligned to mm10 using RNA STAR. I have succes...
• Gene ID from chromosome locus - Cufflinks/Cuffdiff outputs plus other data formats
  Hello, Can anyone help me in how to get the gene ID out of gene locus on galaxy? Thank you,
• Rna-Seq Analysis
  Since the pictures are too big for the mailling list. I will upload it in seperate emails. Dear ...
• gene Id to gene name
  I did DEseq2 on galaxy for my samples after STAR alignment. I got the report and found the first...
• Rna-Seq Analysis
  Dear all, I am using Galaxy for RNA-Seq analysis. I expect two lists: differentially expressed tr...
• Identifying Genes
  I am very new to Galaxy. We have performed a comparative analysis between the transcriptomes of d...
• htseq and cufflinks
  Hi, I have used HTSeq to count the no of mapped reads, the HTSeq gives me the ensemble ids but w...
• How To Find Out The Gene_Id Correspond To Cuff Id
  Dear Everyone: I have got one output file after I run Cufflink which contain gene expression inf...
• How to covnvert gene id to gene names
  Hi, I have been using Tophat, cufflink, cuffmerge and cuffdiff to analyse RNA seq data. I hav...
• Cuffdiff-differential gene expression-NOTEST
  Hi I am just starting up and getting to know and analyze my data from the RNA-seq. I have 2 biol...
• Inconsistency Between Cufflinks And Cuffdiff. This Is Killing Me.
  <> The cufflinks and cuffdiff results are not consistent with each other. This is killing ...
• gene names from ucsc id
  i have cufflink and cuffdiff output. i want gene names in ncbi ids and a tabulated format. i can ...
• Question About Using Replicate Samples And Refrence Ensembl
  I am running RNA seq and while I have to run Tophat how can I include replicates of samples than ...
• GTF usage in Cufflinks
  My problem is that Cufflinks does not recognize the gtf file that I provide. It shows an error th...
• cufflink output and gene id correlation
  hi i am following the basic rna seq pipeline. on my sra ids i have done qc and grooming. i did...
• gene names and gene ids
  hi i have a annotate file of vcf using vcf annotate and in my out i dont have any gene ids thier...
• Batch conversion of ID to gene symbol
  I'm an old school molecular biologist who studies gene expression but is quite new to bio-computi...
• How to get all possible group pairings in cuffdiff- Main
  Hi, I have 4 samples and followed the tophat, cufflinks, cuffmerge and cuffdiff workflow.  I mer...
• gene id missing
  Hi , I run the tophat, cufflinks, cuffmerge and cuffdiff on a human data set. I used h19 as refe...
• Comparing FPKM Values Between 2 Cufflinks Outputs
  Hello, apologies if this is a dumb question, I am relatively new to RNAseq. I have processed 9 sa...