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• Does Tophat Output *.Accepted Hits File Contain Headers?
  Dear All, I want to use the Tophat output files with ".accepted hits" to do analysis outside Gal...
• Evaluating Tophat'S Results
  Hi, I ran TopHat on Galaxy for my RNA-seq data. I want to analyze TopHat's output files, such as ...
• Error "Out Of Memory" When Trying To Retrieve Output
  Hello, I wanted to download the accepted junction .bam file from tophat output of my local instan...
• DiffBind on Galaxy
  Hi, I am trying to perform Diff Bind on Galaxy using output from MACS and bam files for Read and...
• Parameters For Merging Bam Files
  Hi All, I want to merge the Tophat output (Accepted Hits) of Several datasets. I want the merged...
• DEXseq error - "Error in library("DEXSeq") : there is no package called 'DEXSeq'"
  Dear all I want to analyse my RNA-seq data using DEXseq on the galaxy platform. I have made count...
• Using filtered data for TopHat
  Hi, When I extract DRR data using "Extract reads in FASTQ/A format from NCBI SRA," for TopHat, ...
• How to make multiple Tophats inside a workflow to run sequentially rather than simultaneously?
  In my workflow on Galaxy, I have 6 fastq samples to run through Tophats and their output bam fil...
• Troubleshooting: Problem TopHat paired data
  Hey! I´m using TopHat and it works well for 3 of 4 samples. But unfortunately an error occurs whi...
• Cuffdiff Error - sort order of reads in BAMs must be the same
  Hi, I am trying to run Cuffdiff with a Cuffmerged data of 8 files along with their Tophat counte...
• error running DESeq2
  Hello, I am running DeSeq2 on tophat Htseq converted files. The job is marked red with an error,...
• Problem with running TopHat and MARKDuplicates on Galaxy
  To galaxy experts, I would like to ask your advice on some problems I've been encountering with r...
• How many input BAM files for Cuffquant?
  I'm trying to use the Cufflinks v. >2.2.0 workflow, which uses Cuffquant. The Cufflinks docume...
• MPileup output file error
  Hi, I am running a bam file on MPileup, the running process takes more than a day, and then I ge...
• multi bam summary
  Hello, I was trying to use mutibamsummary tool to generate the read coverage for 8 filtered Bam ...
• ChIP-seq mapping with Bowtie for Illumina 1.1.2
  Hi, I mapped my chip seq data with 'Map with Bowtie for Illumina 1.1.2' and used 'Filter SAM or ...
• Local Tophat Error "OSError: [Errno 2] No such file or directory"
  I have created a local Galaxy server to run RNA analysis. I am trying to run TOPHAT on a fastasa...
• 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...
• Tophat2 error when using a custom reference genome
  why everytime tophat is showing error with the fastqsanger files ? "ERROR: An error occurred with...
• reference genome error
  We had downloaded the custom build O_sativa from MSU version7 as our reference genome for Tophat ...
• Job errors at https://usegalaxy.org Galaxy version 17.09 18.01
  Dear Sir, The bam file from tophat is not downloadable it is showing HTTP error repeatedly. Pls r...