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• TopHat Dataset generation errors
  Hello I'm trying to use TopHat in public server for alignment my RNA-seq data that generated fro...
• GFF format not working with tophat
  I am working with pepper genome Capsicum annuum zunla variety (http://peppersequence.genomics.cn/...
• Tophat2 index problem
  I'm trying to align RNA-seq data of wheat genome so i used bowtie2 with large index option to bui...
• Problem with TopHat in Galaxy using data from Nature Protocols
  Hi, I am a graduate student who began RNA-seq data analysis recently. I am having a trouble with...
• Fastq And Index File Upload Problems
  I'm trying to create a RNA-Seq Workflow with Bowtie/Tophat and Cufflinks using a newly assembled ...
• I used tophat and give mistake Error: segment-based junction search failed with err =-5
  In my local galaxy , I used Tool Shed TopHat Gapped-read mapper for RNA-seq data (Galaxy Version ...
• RNA seq peaks
  how to visualize RNA seq peaks (what format) between different conditions in UCSC genome browser....
• TopHat splice junctions
  Dear all, I'm trying to detect alternative splicing events from RNA-seq experiments. I have used...
• working with xls file format
  Hi I would like to use xls file format for analysis of RNA-seq datasets. First I would like to ...
• 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...
• Tophat Error
  Hello, I was trying to run tophat v1.3.2 on SOLID data and I have this erro...
• 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...
• Rna Seq Analysis
  Hi I have a couple of questions regarding RNA seq analysis. My questions are 1.I need to use a v...
• Reference Genome Format For Tophat
  Dear all, I managed to upload to Galaxy a genome of interest in .fasta format from NCIB website. ...
• Genome file for Bam to Bed or Genome Coverage
  I generated BAM (mm9) files in Tophat and tried to convert them to Bedgraphs using the BedTools p...
• "View Details" Of Tophat Alignment
  Hi All, After I finshed Tophat alignment for RNA-seq, I took look at the details of parameters b...
• 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...