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• CummeRbund input from Cuffdiff output
  Hello All I just finished my Cuffdiff on a set of practice data, and I am planning to visualize...
• No output from Cuffdiff
  Hi, I've been running Cuffdiff on Galaxy today, exactly as I did last week (using the same refer...
• Problem with Cuffdiff's field
  Dear Sir or Mandam, I am trying to run Cuffdiff by NGS: RNA Analysis. I succed in uploading my t...
• Please Help With The Settings For Cufflink, Cuffmerge And Cuffdiff
  Dear All, I am looking for the differential splicing events between cell types. Although I got a ...
• RUnning cuffdiff on 2 conditions w/ no replicates
  I have two sets of data; 12 hours control and experiment and 48 hours control and experiment. I a...
• Cuffdiff No isoform FPKM Tracking and differential testing
  Hi All,  my dataset is an RNA-Seq set from illumina; workflow includes Tophat for Illumina ->...
• Jobs not running
  Hi, I set up CuffDiff to run this morning, around 9.30am, and two hours later it's still not run...
• Cuffdiff Errors
  Hello I am having a problem running Cuffdiff on some RNA-seq data. I want to compare 2 of my con...
• Our Deleted and purged Items still look like they are still running and holding up the queue
  Hello, I realised we put in the wrong setting to run a CUFFDIFF so I deleted and purged those and...
• Read_Group_Tracking Files Are Not Enough For Cummerbund Visualisations On Replicates?
  Hi, Cuffdiff in Galaxy produces "read_group_tracking" files. However, I wonder if these files ar...
• gene Symbol from cuffdiff output
  Hi. I received output from cuffdiff which included gene_id, gene and locus for each differential...
• How do I associate a genome with a BAM file?
  I aligned some RNA-Seq reads to a genome sequence using tophat2 and now cuffdiff complains that t...
• Cuffdiff
  Dear All I have simple and question for cuffdiff should we run cuffdif on merge transcript file (...
• CUffDIFF fatal exit code Error 139
  Hi My cuffdiff run does not continue , it stops and says  FATAL error exit code 139(),  My functi...
• error code 139 while running cuffdiff on galaxy
  Though my data set doesnt have replication, it should run right? but running the cuffdiff shows f...
• Cuffdif Output Notest
  Dear all, I have Illumina RNAseq data and want to look for differences in gene expression betwee...