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• Cufflinks tool locally cached 'hg38' malformed; error reads: 'An invalid option was selected for index, u'hg38', please verify'
  Greetings, I am trying to use the Cufflinks tool in the main/public instance of Galaxy to gen...
• Locally cached sequence not detected from DBkey in cuffmerge when using mm10
  Hi, I'm running a cufflinks pipeline on the public server, and I'm having trouble using the loca...
• C: Bias Correction : Locally cached human reference sequence data
  Hello Jennifer, your most answer correctly identified a problem with Cuffdiff returning red boxes...
• mm10 built-in reference genome unavailable
  Hi, I'm trying to run cuffdiff with bias correction: perform bias correction 'yes' -> Refer...
• "Realigner Target Creator" tool on usegalaxy.org Locally cached reference unavailable
  HI  I have a bam file generated using a cached reference  (not a user custom one).  However if I...
• Map with BWA-MEM local cache load option not available
  Reference: https://vimeo.com/123108417 Time location in video: 00:39 This video d...
• Using reference file in Indel realigner under locally cached option
  Hi , I am trying to use indel realigner before somatic variant calling for tumor-normal pair. I ...
• Cufflinks Eference Annotation
  Hello, if I am looking for DE between samples and ran cufflinks without reference annotation, doe...
• 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...
• Reference Genomes do not exist in local Galaxy's Bowtie2
  Want to use reference Genome hg19 for Bowtie2 from a local instance of Galaxy. The pulldown for s...
• Cufflinks duplicate GFF ID error
  I think this is an old but common problem that many people encountered when running the cufflinks...
• Cufflinks in galaxy
  When I am using cufflinks in galaxy the option use reference annotation, when selecting use refer...
• Locally cached annotation not available for featureCounts
  Hi all, For my RNAseq analysis, I am using the featureCounts tool to measure gene expression fr...
• How to get / create GFF files for Cufflinks for Zebra Finch genome (taeGut2) on Galaxy ?
  Hi, I'm trying to perform Cufflink on my local instance of Galaxy. I've installed taeGut2 ge...
• Sam-to-bam in workflow
  I made a workflow in which I am using the tool SAM-to-BAM. I wanted to use a locally cached refer...
• instructions for fetching and install mm10 genome and hisat indexing for local galaxy
  Hi all, Is there a kind soul that could take me through a step-by-step of fetching and indexing ...
• Help W Sam To Bam
  Hi, We're loving Galaxy. This is an excellent interface and set of tools. The issue we're havi...
• Cuffcompare results in an empty file
  Hi, I am trying to run cuffcompare on a cuffmerge file using local galaxy but i am getting an em...
• HISAT2 - no reference genome available
  HISAT2 does not have any options for a built-in reference genome. I need mm10. Source for the r...
• Concatenate locally cached assembly
  I wish to create a custom build of the mm9 assembly by inserting a FASTA file. Is there a way I ...
• How to include ensembl Human annotation FASTA files in Galaxy for cufflinks bias correction
  Hi everyone! I am working on an RNAseq project and have successfully run cufflinks using the Ens...
• Trying to find antisense transcripts. Can Cufflinks in Galaxy specify library type?
  Hello, I am trying to find antisense transcripts, and mapping stranded reads to reference genome...