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• Imported Cufflinks assembled transcripts files not recognized by cuffmerge
  Hello, I've imported two assembled transcript .gtf files from previous Cufflinks analysis into G...
• cuffmerge encounters errors in gtf/gff files
  Does anyone know how to fix the following cuffmerge errors? Initially I thought it's the "refere...
• 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...
• Rna-Sea analysis and cufflinks
  Hello, I am using the following pipeline to analyze my RNA-Seq data to detect differences in gen...
• Cuffmerge Loses P_Id
  Hello, Problem: Cuffmerge loses p_id from reference genome in merged gtf file on Galaxy online s...
• 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...
• 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...
• Issue running Cuffdiff using Cuffmerge gtf output
  I am trying to use Cuffdiff to find significant changes in mRNA transcript expression between two...
• Cuffmerge ValueError merging assembled transcripts
  I am attempting to analyse my first RNA-seq experiment using Tuxedo tools. When I attempt to cuf...
• Extract Genomic DNA error with custom genome
  Hi, I'm new to Galaxy, and I and trying to use the "extract genomic dna" tool. I would like to f...
• Cuffmerge Question
  I'm new to RNA-Seq analysis and think this question must have been asked before, but I can't find...
• Rna-Seq Analysis
  Since the pictures are too big for the mailling list. I will upload it in seperate emails. Dear ...
• Rna-Seq Analysis
  Dear all, I am using Galaxy for RNA-Seq analysis. I expect two lists: differentially expressed tr...
• Gene annotation dataset from Ensembl not recognized by Cufflinks
  Hello Galaxy/Biostars, I am trying to perform RNA-seq analysis using Cufflinks at Galaxy. In ord...
• Extract Spliced Transcripts From Cuffmerge
  Hi All, I have mapped RNA-Seq reads to an unannotated partial genome assembly and assembled them...
• Cuffcompare Or Cuffmerge
  Hi all, I read one paper "Differential gene and transcript expression analysis of RNA-seq experim...