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• SAM to BAM of samtools: It can't find built-in reference genome.
  as the title! I installed data manager of samtools index builder. What a strange affair! SAM_to_B...
• Locally cached Reference genomes not available for cufflinks
  I'm using the cufflinks tool on usegalaxy.org and when attempting to use the bias correction opti...
• Importing Reference Genome Into Galaxy For Tophat2
  Hi, I am new to the field of RNA-Seq analysis. I'd be very greatful if somene could help me with ...
• Content of the built-in hg38 genome annotation available in Featurecounts
  Hello, After executing featureCounts on my BAM file using a built-in genome (hg38) from Galaxy ...
• Loading human genome hg38 reference sequence- completely stuck
  I am running a local version of galaxy (17.09) trying to analyze RNA seq data with Bowtie2, DEse...
• bwa mem index builder error
  I would like to use the BWA mapper tool so I installed the tool "bwa" from "devteam" from main to...
• Problem with Reference genome from history in Tuxedo
  Hi, 1- I am using Tuxedo for tomato. I run the workflow from the shared data. In the TopHat sec...
• GATK Select Variants Reference Genome
  Hi, I'm trying to use GATK Tools Select Variants on VCF files of whole genome sequencing data, ...
• HISAT2-reference genome not available in a local -- data must be installed first
  Hi everyone, When I'm trying to use in my local galaxy HISAT2 for mapping the reads I have an inf...
• Data Files For Fundo Tool In Human Genome Variation?
  Hi, I'm trying to get the HGV tools set up on our local instance, and I've hit a stumbling block...
• Can't use cached bed file
  Hey, I wanted to have built-in BED files specific to the genome references that I added to my lo...
• hisat2 index issue (I think)
  Hi all, I used the hisat2 index builder data manager to create a hisat2 reference for a local ga...
• Built-in indexes not working in Local Galaxy Instance
  Hi, I've just finished setting up a local Galaxy instance and everything works fine except for b...
• sam to bam - Galaxy version 17.01
  Hi All First of all I am not a bioinformatician, I'm looking at someone else's test workflow. I ...
• Cuffmerge Question
  I'm new to RNA-Seq analysis and think this question must have been asked before, but I can't find...
• CloudLaunch can't attach an instance to my volume after I increased the disk size
  Hi, I'm working with a local Galaxy (v. 17.05) in EC2, managed by CloudLaunch. I increased the s...
• I can't choose a "reference transcriptome"
  I'm trying to use Salmon Transcript quantification and I can't choose a reference transcriptome. ...
• How to add a new dbkey (publicbuilds, manual_builds, builds.txt, data manager)
  What is the current method I should be using to add builds to galaxy (galaxy dist from 10/6/2014)...
• Quality metrics of ChIP-seq BAM files??
  Hi all, I'm a real beginner in the field of ChIP-seq analysis and bioinformatics in general (so ...
• featureCounts jobs will not submit unless input BAM(s) have the "database" metadata assigned
  Hello, I am trying to run featureCounts on my BAM file using a built-in genome from Galaxy. I wro...