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• Automatic BAM Index creation but tool is unsuccessful in identifying index
  Hello Everyone, I am currently working on a few tools in galaxy which require both a bam and bam...
• BAM index file download leads to Server 500 error
  I am trying to align reads to the TAIR10 Arabidopsis genome with TopHat v2.1.0 (I have an old pro...
• Problem With Bam And/Or Bai Files
  Hello Galaxy Team,   I have been using Galaxy for SNP detection for with great success. Basically...
• HISAT2 Output in Galaxy vs Command Line
  In galaxy, I am given a BAM and BAI file. Does galaxy implement the sorting and index function th...
• Output of FLASH can't be read by other tools?
  Hi, I have used FLASH to assemble some reads. They are still in FASTq format. However I can't ge...
• .Bam File Upload And Use Problem
  Recently I was trying to use Galaxy for my data analysis but ran into problems..... Condition: I...
• Automatic BAM indexing
  Dear community, is there a way to modify the default way Galaxy creates the index *.BAI files? W...
• Split barcodes tool
  Hello,     I am trying to use the split barcodes tool in Galaxy. For some reason, it does not se...
• featureCounts doesn't recognize Rat annotation file in history, what am I doing wrong?
  Dear Experts, I use Htsat2 output file for running feature-counts, but when I set up the run Gala...
• TopHat from Galaxy local instance do not recognize available fastq files.
  Hi there, I am probably missing something obvious here. My local Galaxy TopHat does not recogniz...
• Problem in converting Bam to Bai files
  Hi, In last sessions, I had problems with conversion of Bam files to Bai (error message). Could ...
• GTF usage in Cufflinks
  My problem is that Cufflinks does not recognize the gtf file that I provide. It shows an error th...
• GTF file is not recognized
  Hello, I am trying to align my hits with a GTF file that I upload from Ensembl, however it is no...
• gtf file error
  Dear all, My reference genome is Duck, not index in Galaxy reference genome. So i downloaded fast...
• Problems with Tophat/Tophat2 on local server
  I'm having problems running Tophat on my local galaxy instance (I'm running it via biolinux 8).  ...
• Trouble with samtools mpileup when I supply my own reference genome
  I've been working on Galaxy to run samtools mpileup function. When I use the supplied reference g...
• Tophat not recognizing the ref genome I loaded
  I am trying to run Tophat as I did in a previous analysis using the same ref genome. It is a fas...
• fastq files are't recognized by tools
  Hey, I'm looking forward to do some NGS analysis and would like to use your provided NGS tools. ...
• Problem Uploading Bam And Bai Files
  Hi, I've searched the archives and cannot find my situation. I have an Illumina MiSeq dataset wi...
• bam indices fail to download
  I've recently run a workflow that includes Tophat on several datasets. I can download the result...