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• Problem with using CuffMerge in Galaxy
  Dear all, I want to find differential expressed genes between two RNASeq samples in Galaxy. I w...
• Rna-Sea analysis and cufflinks
  Hello, I am using the following pipeline to analyze my RNA-Seq data to detect differences in gen...
• Cuffcompare Or Cuffmerge
  Hi all, I read one paper "Differential gene and transcript expression analysis of RNA-seq experim...
• cuffmerge does not recognize gtf's
  Cuffmerge does not recognize my assembled transcript files. Says "No GTF dataset collection avail...
• Cuffmerge "Matched on error" - Check for problematic input format
  Hi, This is my first time analyzing RNASeq data. I mapped and aligned my reads using tophat and...
• Cuffmerge
  I am analyzing RNA-seq data and I ran Cufflinks with the genes.gtf as a reference annotation guid...
• Cuffmerge Question
  I'm new to RNA-Seq analysis and think this question must have been asked before, but I can't find...
• Cuffmerge ValueError merging assembled transcripts
  I am attempting to analyse my first RNA-seq experiment using Tuxedo tools. When I attempt to cuf...
• blast2go ontologies comparison
  Hi, i posted this question earlier also but received no feedback, kindly help.   I want to com...
• Issue running Cuffdiff using Cuffmerge gtf output
  I am trying to use Cuffdiff to find significant changes in mRNA transcript expression between two...
• 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...
• Differentiating between Replicates and Conditions - Cuffdiff
  Hello I am new to RNA-Seq analysis and am struggling a bit with setting up the CuffDiff I have ...
• Cuffmerge fails to merge gtf files
  Hello, I am trying to merged to assembled transcripts produced by cufflinks using cuffmerge. I ...
• Cuffdiff
  Dear All I have simple and question for cuffdiff should we run cuffdif on merge transcript file (...
• No gtf dataset collection available in cuffmerge
  Hi, Cuffmerge won't allow me to add all four of my Cufflinks-generated GTF files for merging. Un...
• Erorr with runing cuffmerge
  Hello I am doing RNA-seq analysis, I am trying to run cuffmerge for assembled transcripts files...
• 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...
• Cuffmerge Error: Duplicate Gff Id Encountered
  Hello, I was doing a RNA analyse and I wished to compare the transcription and expression of two ...
• 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...
• Transcriptome assembly with Cufflinks
  Hi Biostars community, I did a transcriptome assembly using Cufflinks with a bam file aligned by...
• How Should I Include Biological Replicates In Cufflink/Cuffdiff?
  Dear team, I have a few questions regarding RNA-seq data analysis. I want to compare transcripto...
• htseq and cufflinks
  Hi, I have used HTSeq to count the no of mapped reads, the HTSeq gives me the ensemble ids but w...
• problem inputing additional input gtf files in cuffmerge
  I am in usegalaxy.org and I want to merge 4 assembled transcript gtf files created using cufflink...
• Cuffcompare successful but generate empty files.
  Hello friends I am currently doing RNA-seq for 3 datasets (obtained publicly through NCBI-SRA...