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• How many input BAM files for Cuffquant?
  I'm trying to use the Cufflinks v. >2.2.0 workflow, which uses Cuffquant. The Cufflinks docume...
• Tarcking ID in cuffnorm output and TestID (geneID) in cuffdiff output, are they the same?
  Dear all, I found in the output of cuffnorm there was no locus information corresponding to my d...
• How to incorporate quantile normalization within a pipeline?
  Hi Biostars, How to perform quantile normalization in a pipeline on biostars? Is this done by cu...
• Segmentation and fatal error: Exit code 139 when running CuffDiff/CuffQuant/Cuffnorm
  I have downloaded the latest version (2.2.1.3) of Cuffdiff/Cuffnorm/Cuffquant on a local instance...
• cuffquant job taking way too long
  Hey, so Ive been trying to run a cuffquant job for about 72 hr. Its still in the queue and nothin...
• What to do with Cuffquant .cxb files
  I would like to get a raw RNA-Seq counts matrix from the results of the Tophat alignment to a ref...
• RNA-Seq High Expression Genes Lost
  Hi I'm noticing that after running my BAM files through CuffDiff and CuffNorm that some genes th...
• space usage increase without any jobs running
  Hi, I have jobs for Cuffquant and Cuffdiff that have been in the que since Friday and Saturday. ...
• CuffDiff not working with CXB files
  Hi when attempting to run CuffDiff with Cuffquant files, all the conditions end up loading condi...
• Cuffquant errors after using HISAT2
  Hi, I have 2 sequence reads archive and I want to do some RNA-Seq analysis on them. Archive 1 :...
• Need help with "Cufflinks" tool
  Hi, How long does it take usually that GALAXY upgrade with a new version of Cufflink (version 2....
• Tophat version not available in toolshed
  I have been using a nice workflow on usegalaxy.org server and we are now migrating to our own loc...
• Uploading .cxb files
  Greetings, I am trying to upload some cuffquant output files (.cxb) to usegalaxy.org using ftp. ...
• Error submitting job on a local Galaxy: Cuffquant version 2.2.2.1
  Hello. I am a new (and only) administrator for a private Galaxy installation that has been in use...
• Error in Cuffdiff analysis with reference genome build
  Hello All, I am using cuffdiff for my differential gene expression analysis. I am doing three co...
• Cuffdiff Error on Galaxy??
  Hi, I am trying to run cuffdiff on Galaxy and I keep on running into the same error: Fatal error...
• Cuffdiff Error after cuffmerge or cuffcompare
  Hi everyone, I'm doing a transcriptome of zebrafish, 2 replicates for each condition of 3 conditi...
• How to get gene sequences (DEGs) not transcripts sequences?
  Hello, my name is one of Galaxy user in Korea. I conducted cuffmerge -> cuffquant -> cuff...
• Error while running cuffdiff "Fatal error: Exit Code 1()"
  Hello, I recently posted about having problems with cuffdiff (https://biostar.usegalaxy.org/p/18...