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  Hi everyone, I am working on RNA-seq data. First, I mapped the reads to the reference transcri...
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  Hi, I have run Cufflinks on my zebrafish RNAseq reads mapped using Tophat2. The Cufflinks output...
• Multiple fastq file for mapping with Bowtie2
  Hi,   I have some amplicon sequences for 144 samples that I would like to map on to a reference...
• Hisat2 to cufflinks
  Hi, Recently, I tried use hisat2 to mapping RNA-seq, then use cufflinks to measure the gene expr...
• Cufflinks Returned 0 Value In All Rpkms
  Hi I have been trying to analyze a rat Solid SRA but I encountered a problem: cufflinks gave me ...
• Strand Specificity
  Dear All, I am trying to analyze my RNAseq data by TopHat-Cufflinks package based on Galaxy. I u...
• Galaxy Reference Genome
  Hello, Galaxy Main 1.) I am having trouble adding annotations to my Tophat and Cufflinks tools....
• Problem With Repeated Genes In Cuffdiff'S Output
  Hi all, I am working on RNA-seq using TopHat/Cufflink/Cuffdiff for differential gene expression a...
• Blank Cufflinks output
  Hi! I am conducting an RNA-seq analysis with Saccharomyces cerevisiae-derived data. In my workfl...
• Variant mapping workflow and tutorial in Galaxy
  Hi, I have a zebrafish mutant that I am trying to map. So I did the mapping crosses and sequenced...
• sam to fastq
  Hi I have mapped PE reads to a custom build genome using bwa and converted the sam output to bam...
• Cufflinks Gene Transcripts
  Hi I have been experimenting with Bowtie and Cufflinks and I now reach a point where it appears t...
• TOPHAT MAPPED READS
  Hi, i am using the RNA seq pipeline for transcriptome analysis. i ahve the annotation anf gff fi...
• Tophat Mapping And Cufflinks Output Issues
  Hello Galaxy Users- I've been using the Main Galaxy server to work on an RNA-Seq project for a n...
• 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...
• same gene with multiple expression from cuffdiff
  Hello, I ran tophat-cufflink-cuffdiff of my RNA-seq, and got the cuffdiff "gene differential exp...
• Trying to find antisense transcripts. Can Cufflinks in Galaxy specify library type?
  Hello, I am trying to find antisense transcripts, and mapping stranded reads to reference genome...
• CuffDiff error, "Uncaught exception in exposed API method," job runs, but no results
  Hello, I’ve run into a problem while analyzing some RNAseq data on usegalaxy.com. I am looking...
• Running Cufflinks On Bacterial Rnaseq Data
  I am attempting to run Cufflinks on Galaxy main to analyze my E. coli RNAseq data. I have mapped...
• Using Cufflinks v. 2.2.1.5
  Hello community, Let me lead with, I have never been able to successfully run the tophat2-cuffli...
• How to run a multiple hypothesis test on genomic data in galaxy
  Hello! I am trying to answer some very broad questions with some chromosomal genomic data. So fa...