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• How to include ensembl Human annotation FASTA files in Galaxy for cufflinks bias correction
  Hi everyone! I am working on an RNAseq project and have successfully run cufflinks using the Ens...
• Add Reference Genome When Designing A Workflow
  Hello Scientists, I have been running my workflow manually and when I use CuffLinks and CuffDiff...
• Cuffmerge
  I am analyzing RNA-seq data and I ran Cufflinks with the genes.gtf as a reference annotation guid...
• Cufflinks "perform quartile normalization" issue
  Hello, I'm trying to run cufflinks in Galaxy (Galaxy Tool Version 2.2.1.0) with the quartile nor...
• Bias Correction : Locally cached human reference sequence data
  For a cufflinks run, Galaxy detected up human (homo Sapiens) hg19 for the locally cached referenc...
• Re: Running Cufflinks On A Genome Without A Bowtie Index
  Noa, Using your FASTA in Tophat and Cufflinks is the correct approach. You don't need to provide...
• Locally cached Reference genomes not available for cufflinks
  I'm using the cufflinks tool on usegalaxy.org and when attempting to use the bias correction opti...
• 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 ...
• Reference Genome unable to be detected on cuffdiff/cufflinks & Empty CuffDiff output files
  Hi, I am currently following the tophat->cufflinks->cuffmerge->cuffdiff pipeline. Every...
• Cufflinks Set Parameters
  Hi,   It's the first time for me to use cufflinks in galaxy, two choices confused me as follows: ...
• Cufflinks assembles very small number of transcripts from RNA-seq data
  I mapped RNA-seq data to reference genome and tried to assemble transcripts using cufflinks.It is...
• mm10 built-in reference genome unavailable
  Hi, I'm trying to run cuffdiff with bias correction: perform bias correction 'yes' -> Refer...
• C: Bias Correction : Locally cached human reference sequence data
  Hello Jennifer, your most answer correctly identified a problem with Cuffdiff returning red boxes...
• about compute and correct GC bias
  Hello I am having a trouble running the compute GC bias on a BAM file aligned by BWA-MEM. The err...
• Compute and correct GC bias
  Hello I am having a trouble running the compute GC bias on a BAM file aligned by BWA-MEM. The err...
• Locally cached sequence not detected from DBkey in cuffmerge when using mm10
  Hi, I'm running a cufflinks pipeline on the public server, and I'm having trouble using the loca...
• Cuffdiff not working in Galaxy
  Hi, I'm trying to run cuffdiff as part of an RNA-seq project, and it's not working. I've tried l...
• Re: Cufflinks Merging More Than One Transcript On Bacterial Genomes
  Noa, I'm not sure that folks on this list have much experience with bacterial transcriptome ana...
• Issues with Using CuffDiff Tool in Galaxy
  Hi,   I am analyzing microRNASeq data. My pipeline is qc reads, bowtie for alignment, cufflinks...
• CuffDiff: Unknown Error
  Hello All, I'm using CuffDiff online at usegalaxy.org and keep running into  "Unknown error occu...