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• Deseq2 with 0 lines in output
  Hi, Using Galaxy main (usegalaxy.org) I have been happily runnning Salmon followed by Deseq2 to ...
• How to get only paired end or single end uniquely mapped reads with Bowtie2?
  Hello, I am using bowtie2 on galaxy to map ChIP-seq single end and paired end libraries to a ref...
• Installing Sailfish or Salmon
  Hi everyone, We are setting up a Galaxy instance (Cloudman, EC2) to teach an RNA-Seq class and w...
• Re: Output File For Bowtie Suppressed Reads (-M/--Max)
  Hi all, I'm running into a problem with the output from bowtie mapping for illumina reads. I'v...
• How can I improve my mapping alignment rate with MiSeq 2x300 bp paired-end reads?
  Edit 1: it appears I have misinterpreted the raw data, which in turn led to my poor results. The ...
• Salmon not working
  I have not been able to get Salmon to work for the past four days. Following the instructions of ...
• How To Use Collapsed Sequence Files In Mapping And Displaying
  I found that there is a "collapse" tool under FASTA manipulation, which will significantly shorte...
• Fatal error with DESeq2 when processing TPM-based Salmon files and using a tabular transcript-gene mapping file
  Hi there, I have used Salmon to map RNAseq reads to a transcriptome. I then proceeded to anal...
• Bowtie Seed Length (-L) And Non-Unique Reads Mode (M=-1)
  Hi there, I have two questions regarding alignment using Bowtie: 1. Is there a way to set the S...
• Question About Samtools Filter In Galaxy
  I have a sam file after running BWASW and want to extract unique (alignments that are aligning on...
• extract only unique mapped paired end reads
  Hello,  I aligned paired end reads with bwa 0.5.9. Next, I would like to extract only paired end...
• Salmon: Error while indexing Human transcriptome file
  Hi there! I downloaded what I hope to be a human transcriptome data file from biomart. I select ...
• Job Submission Failed
  Hi, I keep getting a "Job Submission Failed. The Server could not complete the request. Please co...
• I can't choose a "reference transcriptome"
  I'm trying to use Salmon Transcript quantification and I can't choose a reference transcriptome. ...
• Tab database sort and retrieve unique records
  Hi Galaxy, After retrieving taxonomic representation, I would like to select unique data set fro...
• what is a "Tabular file with Transcript - Gene mapping" in DESeq2?
  I have RNA Seq data from two conditions using a non-model organism. I constructed a trinity assem...
• problems with PE reads upload
  Hi. I am new in galaxy and I am having problems when uploading samples. I am uploading PE reads (...
• Using Bwa To Map Without Any Mismathces
  Hello, We have a sample containing several bacterial species and we want to uniquely map RNA-seq ...
• Salmon tool error: libgomp.so.1 missing
  I started a salmon job on the main galaxy site and I got the error: Fatal error: Exit code 127 (...
• How to count unique short sequences in FASTQ
  Hi, I wonder whether there is any tool that I could use to output the number of unique reads. I d...