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• 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...
• Cufflinks in galaxy
  When I am using cufflinks in galaxy the option use reference annotation, when selecting use refer...
• how to analyze the results and am not able to add my datasets using visualisation after Tophat
  Hi,   I am new to this interface. Trying to run published histories and datasets. I am not able...
• problem with TopHat
  I am very sorry to disturb you with these questions, however I am trying to align 4 bam files (af...
• Tophat in Cloudman: missing built-in genome
  Hell all, After several days of struggling, I finally managed to set up a Galaxy instance in Clo...
• Error Message Saving File From Galaxy
  I had problem in the past saving sam file from Galaxy's floppy sign and at that time Jen mentione...
• running of the files after uploading
  Hi... I am unable to run the files after uploading. The uploading is done but on the left side on...
• Tophat taking for a long time
  I am running Cufflinks of a couple of dozens of RNAseq Bam files from using mm9 as a reference. F...
• Cloudman instance: Tophat error
  Hello community, I am encountering the following error when I try to run Tophat Galaxy Version 0...
• Merge Bam files
  I am trying to merge 3 .bam files (different alignments of the same ChIP-seq run), one has 5.9M r...
• How to find and extract novel transcript from cufflink and cuffdiff.
  I am analyzing Arabidopsis Rnaseq data. I was running Tophat and cufflinks, but after that I don'...
• Difference between Fastq and Fastqsanger?
  Hi,  Can somebody briefly explain the difference between fastq and fastqsanger files in Galaxy? ...
• long running time on freebayes with a bam file
  Hi, I am using Galaxy freebayes to call variants on a WES bam file. It apparently takes very long...
• 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...
• upload 1 BAM file (2.6G) in queue since 4 hours
  Hello, I am trying to upload one single BAM file as a test, through ftp. I don't have other job r...
• Editing reference genome for TopHat on Trapline
  I am trying to use the Trapline workflow for RNA-Seq data, and have read the manual. I want to ed...
• unable to load zebrafish GTF/GFF3 files from current history into any of the RNA analysis tools
  I am analyzing zebrafish RNA seq data, I am able to upload the fastq files, use trimmomatic, alig...
• 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...
• Tophat jobs exceeding maximum allowed job run time
  Hello, I have a question regarding the mapping of RNA-seq data. I am hitting a wall, because som...
• Hisat2 to cufflinks
  Hi, Recently, I tried use hisat2 to mapping RNA-seq, then use cufflinks to measure the gene expr...
• suite_samtools_1_2 EOF marker absent error
  Hi all, so I'm experiencing a problem running SAM-to-BAM using samtools 1.2 from a toolshed insta...
• What is the purpose of Cufflink and Cuffmerge?
  Hi guys, I am new to the galaxy server, and I want to analyse my RNA-seq data with the following...