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• HISAT problem on local galaxy
  Dataset 33: HISAT on data 3Tool execution generated the following error message: Fatal error: Ex...
• Cloudman instance: Tophat error
  Hello community, I am encountering the following error when I try to run Tophat Galaxy Version 0...
• hisat2 index issue (I think)
  Hi all, I used the hisat2 index builder data manager to create a hisat2 reference for a local ga...
• Custom tool in local bio Linux Galaxy does not work.
  For example, i want to have an opportunity to convert sam to bam via samtools in my local galaxy....
• Cannot download a bam dataset list
  Hi! I am having trouble trying to download a list of pairs from a mapping (bam files) either usi...
• AddOrReplaceReadGroups Fatal error
  **Dear Biostars/Galaxy Friends, Hi** I am using `AddOrReplaceReadGroups` in online galaxy for t...
• stringtie error in refernce genome file
  hi i m working on human datasets i tired running stringtie with the bam file from hisat....i get...
• SAM to BAM conversion ERRORS
  I want to convert a SAM file to BAM file. I've used SAMtools in Linux command-line for this. I am...
• User Reference Vs. Built-In Index
  Hi. I created a workflow to map IGA reads using bowtie and generate a pileup at the end. The work...
• error when upload tool in tool shed.
  Hi all,   I integrate the SoftSearch tool in local galaxy successfully. Then I upload my tool i...
• Cufflinks Fpkm Problem
  Hi£º I use the solid PE sequencing data and mapped with the bioscope tools(AB company supported) ...
• Problem for converting SAM file to BAM file
  Hi,  Recently,galaxy always reports error when I convert filtered SAM file to BAM file by using ...
• galaxy biomina RSeQC bam/sam mapping stats error
  I am trying to run the Galaxy Biomina RseQC BAM/SAM mapping quality stats I have selected my upl...
• Error while running cuffdiff "Fatal error: Exit Code 1()"
  Hello, I recently posted about having problems with cuffdiff (https://biostar.usegalaxy.org/p/18...
• Alignment rate differes using hg19 and hg38
  I have some RNA-seq fastq files.I'm using HiSat to align the fastq files. To do so, I use the bui...
• Problems with Bamtools: Filter BAM
  Hi, I seem to have a problem with filtering merged BAM files following a recent update. I am tr...
• Unknown error on HTseq_count
  Hi, I’m trying to do RNA_seq analysis with Galaxy. I upload the hg38 iGenome from illumina to my ...
• bam indices fail to download
  I've recently run a workflow that includes Tophat on several datasets. I can download the result...
• Problem to upload files to a data library in Galaxy local
  Hi, I've recently installed galaxy locally on my computer, I got it run but I can't upload files...