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• mm10 built-in reference genome unavailable
  Hi, I'm trying to run cuffdiff with bias correction: perform bias correction 'yes' -> Refer...
• 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...
• Cuffdiff Fatal error: Exit code 1 () Error: number of labels must match number of conditions number of labels must match number of conditions
  Hi! I ran into a problem using Cuffdiff. (I am using a local version of galaxy). When I try to ...
• Mapping Paired End Reads With Tophat
  Hi all, After mapping, I used IGV to have a look at the mapping. There are a lot of mapped read...
• New Cuffdiff- No Result Files
  Hi, I have this week used the new wrapper version of Cuffdiff that you provide that should now i...
• Splitting Biased Paired End FASTQ data
  The FASTQ splitter in Galaxy warns that the tool only works if Paired-end data has equal length r...
• Please Help Me Check The Quality Of The Tophat Mapping To Reference Genome
  Dear All, I ran "Flagstat" under "NGS: SAM Tools" to check the quality of the Tophat output (the...
• 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...
• Cuffdiff Changes
  Hi, I am wondering why Cuffdiff suddenly gives many more significant DE genes? I have used same ...
• 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...
• Bias Correction : Locally cached human reference sequence data
  For a cufflinks run, Galaxy detected up human (homo Sapiens) hg19 for the locally cached referenc...
• 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 ...
• cuffmerge for single end and paired end
  is it correct to merge the single end and paired end data together in cuffmerge? if yes then why ...
• Fastq Splitter Produced Empty Dataset, Please Help
  I have problem to split a paired-end FASTQ dataset into two separate datasets. In order to explai...
• Error using stringtie - AttributeError: 'NoneType' object has no attribute"
  Hi, I have **RNA-seq data** and I am interested in whole gene expression results but also transcr...
• Best Tophat parameters for splicing
  Hey I was wondering if there are any key parameters to consider for Tophat to maximise my chanc...