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• Find exogenous sequences like EGFP in RNA-seq data
  Hi, I am mapping some data from EGFP+ and EGFP- samples. I want to confirm that they are what I ...
• Loading VCF into a local IGV fails with metadata error during data prep step
  Although my genome sequence is part of the list of options thanks to custom build, the link to di...
• Delays with Processing Custom Genome Builds
  Has anyone else been experiencing very long wait times when creating custom genome builds? I hav...
• Unspecified Genome Build
  I'm trying to use the "Extract Genomic DNA" feature from "Fetch Sequences" on Cufflinks-assembled...
• Extract Genomic DNA error with custom genome
  Hi, I'm new to Galaxy, and I and trying to use the "extract genomic dna" tool. I would like to f...
• HISAT2 and custom reference genome
  Hi! I want to perform HISAT2 aligment in galaxy using a custom genome. In this case I want to us...
• visualize tophat output on custom (zerbafish) genome, output not in list
  I am a beginner so this may be a basic question....I have taken 2 rnaseq datasets from the geo da...
• Need help with "MPileup" tool
  I am trying to get SNPs and indels from a bowtie 2 on Illumina reads matched to the sinorhizobium...
• How to add my reference genome to use RNA STAR in usegalaxy.org
  "If your genome of interest is not listed, contact the Galaxy team (--genomeDir)" It is my first ...
• built-in genome for HISAT2 not available
  I am trying to map fastq to mm9 genome using HISAT2. But the drop-down list of built-in genomes i...
• Fasta Files from FTP sites
  Hi, I have used FTP to download the mouse genome from NCBI, Ensembl, and UCSC. When I navigate t...
• bwa not recognizing fastq files
  I am trying to map a set of fastq sequences to a custom genome, using BWA. The two setrs of trip...
• Need help with "Create a BedGraph of genome coverage" tool
  Hi there I am trying to calculate the coverage of my alignment based on the BAM file using "Crea...