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• Poor overall alignment rates
  I am having problems with the alignment process for some data that I obtained through NCBI GEO da...
• hisat2 index issue (I think)
  Hi all, I used the hisat2 index builder data manager to create a hisat2 reference for a local ga...
• TopHat alignment failure
  It has been two days I can't align my data. TopHat gives an error message few seconds after the e...
• Reference Annotation error using HISAT2
  I keep getting a reference annotation error when I run cuffdiff using HISAT2 alignment files. The...
• Ngs With Arabidopsis Thaliana Built-In-Index
  Hi all, I've been having trouble running my Arabidopsis thaliana NGS pipeline in galaxy. Specifi...
• 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...
• variable, low alignment rates with HISAT2
  Hello, I have some single end mouse RNA sequencing data that I would like to use galaxy to analy...
• sample numbering in edgeR
  Dear Sir/madam I am running edge R and keep running in to two ietems, hopefully you can help me....
• Error: htseq-count exceeds memory buffer, Solution: Set sort option on tool form to Yes
  Hello, I am dealing with RNA-seq data and I was successfully able to align my raw FASTQ data to t...
• HISAT error msg or 0% alignment.
  Hi, I'm very new to Galaxy and RNA-seq in general. I can't seem to figure out why we are getting ...
• Can contamination cause alignment errors and how can I trim contaminants away?
  Hello Galaxy Team, Sorry if this question is all over the place. I have been trying to align ...
• Problem with running tophat2
  Hello everyone, this is the first time i'm trying to run tophat2 on a computer cluster, which a...
• Need help with "VCFgenotype-to-haplotype:" tool
  Hello, I have been trying to convert a VCF file downloaded from 1000genomes (VCF v4.1) using thi...
• Cuffdiff Errors: "Loading reference annotation" and "Inspecting maps and determining fragment length distributions".
  Hey, I have 30 individuals that have two samples each. I've had no problem running Cuffdiff bet...
• Filtering BAM files from HISAT2
  Hi. I am new to rna-seq and I have a couple of quick questions. My input was paired-end non-stran...
• TopHat error message
  Hi, I've been trying to run TopHat on my RNAseq data. I ran my data through FastQC and then Trim...
• Chrdecoy Error In Trackster
  Hello, I’ve been using Galaxy for RNA-seq analysis. Many thanks for this great resource! I hav...
• Problem with running TopHat and MARKDuplicates on Galaxy
  To galaxy experts, I would like to ask your advice on some problems I've been encountering with r...
• align.seq mothur error
  Hi. i am new to galaxy. i'm trying to align my NGS samples based on galaxy 16s Microbial Analysis...
• Tophat in Cloudman: missing built-in genome
  Hell all, After several days of struggling, I finally managed to set up a Galaxy instance in Clo...
• Problems with HISAT2
  When I use HISAT2, it fails with the error message: cannot find 'read_f'. I used it at the beginn...
• Adding a reference genome to a local Galaxy
  Hoping to find some Galaxy Dev team experts. I am trying to add hg38 to the HiSat2 tool so that t...
• Keep getting "This is a new dataset and not all of its data are available yet"
  Hi there, I am keep getting the message "This is a new dataset and not all of its data are avail...