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• Get multimapped reads from STAR in Galaxy.
  Hi, Using RNA STAR in Galaxy to map my yeast read back to the genome: (single end reads), I'm g...
• 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...
• RNAseq data to be processed in two ways: (i) mapping to de novo Trinity-based transcriptome and (ii) mapping a relatively new genome
  Hello all, I am new to RNAseq data and learning this process step by step, so I have a few quest...
• Cuffmerge Question
  I'm new to RNA-Seq analysis and think this question must have been asked before, but I can't find...
• Bam Files
  Hi - I have a set of 454 reads that have been trimmed and converted to BAM format using Galaxy, ...
• can't upload data via FTP
  Hi, I'm recently doing mapping using Galaxy. I have uoloaded my fastq and reference genome data ...
• Trackster Error Chrom/?.Len , No Such File Or Directory
  I have my own genome fasta file containing 1 chromosome with a modified header so that it looks l...
• How to add a genome indexed at https://usegalaxy.org to IGB (when it is not already natively included)
  Hello, I have been using Galaxy Main to map WGS data from E. coli. I have tried several mapping ...
• Bowtie: Outputting Unmapped Reads
  I was hoping this question had been asked, but I haven't been able to find it. I want to output ...
• Adding a reference genome to local Galaxy
  Hello I am using a local instance of Galaxy to call variants among six sets of reads from mouse ...
• 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 ...
• Bowtie Reference Genome
  Dear galaxy users, I am trying to map some multiplexing bisulfite PCR data (Illumina) to o...
• Can a genome that's been released be added so I can map against it
  Hi there, I will be mapping my RNAseq reads to a genome of interests soon. Mapping with Bowtie2 ...
• Gain Sequences After Mapping Reads To A Reference Genome
  Hi all, I would like to know if mapping reads to a reference genome, through galaxy, can generat...
• How secure is Galaxy?
  Hi all, I was wondering how secure cloud Galaxy is if I'm using the default space provided by Ga...
• RNA STAR Gapped-read mapper for RNA-seq data
  Hello Galaxy team, I am trying to map an RNAseq data to human reference genome using the RNA STA...
• Using BWA with Illumina data and metagenomic "reference genome"
  Hi, I'd like to try using BWA to align Illumina reads to some contigs a collaborator made from my...
• Alignment and consensus from mapped reads (Ion PGM - Ampliseq Custom Panel)
  I have an Ion Torrent Ampliseq Custom panel of 28 Culex genes that I have run on our Ion PGM. It'...
• input file types to DESeq on the cloud
  Hi there, I've had a go at using the Ratsch lab DESeq tool but it seems to require your input fi...
• Workflows don't execute after successfully being invoked at https://usegalaxy.org -- RESOLVED
  I've been trying to execute two workflows on several of my datasets, but they won't execute. I ge...
• Evaluating Tophat'S Results
  Hi, I ran TopHat on Galaxy for my RNA-seq data. I want to analyze TopHat's output files, such as ...