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• HiSAT2 alignment to GRCm38? in Galaxy -- where to find mm10 reference annotation
  I am doing an RNA-seq experiment and I ran HiSAT2 with the mm10 reference genome. Then in order t...
• Gene annotation for cuffdiff/cufflink
  I was wondering how to get gene "name" annotated to the cuffdiff. I used mm10 as the template, an...
• Problem running CollectRnaSeqMetrics
  Hello, I am trying to run Collectrnaseqmetrics in usegalaxy (toolshed.g2.bx.psu.edu/repos/devtea...
• Problem with Annotation Regions using ANNOVAR Annotate VCF
  Hello, I'd like to use ANNOVAR Annotate VCF via Galaxy Web (Galaxy Version 0.2) to annotate vari...
• Cannot perform a Liftover.
  Hi, I am trying to perform a liftover from mm10 to hg10 using cufflinks assembled transcripts GT...
• 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...
• Chromosome Coordinates to Annotation
  Hello, If I have specific chromosome coordinates, how do I find out if this region is Exon or In...
• No case matched value Error with use of conditional statements
  Hi, I am trying to integrate my own tool into galaxy on a local instance. My galaxy UI is design...
• Problem with the tool: Extract Genomic DNA
  Hi! I'm new with bio-info analysis and I'm doing my first ChIP-Seq analysis with Galaxy. I follow...
• how to merge multiple cufflink data in one file
  how to merge multiple cufflink data in one file. what i am expecting is rows will represent gene ...
• hisat2 index issue (I think)
  Hi all, I used the hisat2 index builder data manager to create a hisat2 reference for a local ga...
• How to upload Mouse reference genome mm10, in Fasta format to My Galaxy History
  I tried to use an imported "tuxedo protocol" RNA-seq pipeline from public workflows. I found mous...
• Annotation file that contains XLOC_ Cuffdiff Gene_ID and Gene Symbol etc.
  I am looking for a stand alone annotation file for mm10 genome that contains all Cuffdiff XLOC_ G...
• Gene annotation dataset from Ensembl not recognized by Cufflinks
  Hello Galaxy/Biostars, I am trying to perform RNA-seq analysis using Cufflinks at Galaxy. In ord...
• How to get counts for transcripts for all replicates
  Hi BIOSTARS, I have lots of samples that have been aligned to mm10 using RNA STAR. I have succes...
• Converting Ensembl GRCm38 gff to make it into UCSC format
  I am using STAR to align my RNAseq reads to UCSC mm10 mouse genome on Galaxy. Galaxy has UCSC mm1...
• 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...