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• How do I associate a genome with a BAM file?
  I aligned some RNA-Seq reads to a genome sequence using tophat2 and now cuffdiff complains that t...
• Genome build accession for Galaxy build-in genomes
  How can I find exact genome build (NCBI accession number, like GCA_000001405.17) for build-in gen...
• Downloading GFF files from NCBI
  Hi: Can someone help me figure out how to import a genome from the NCBI website into Galaxy in a...
• How to add and use a custom reference genome
  How to import my genome (maize B73v3) into galaxy? I have B73v3 in custom-run UCSC genome browse...
• How Do I Import Protein Coding Genes Location From Ucsc?
  I have to import into Galaxy annotations of coding genes from the UCSC genome browser and then us...
• Importing Reference Genome Into Galaxy For Tophat2
  Hi, I am new to the field of RNA-Seq analysis. I'd be very greatful if somene could help me with ...
• Bam Files
  Hi - I have a set of 454 reads that have been trimmed and converted to BAM format using Galaxy, ...
• 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...
• Could Not Find The Refseq From Database List
  Hi, I am using Galaxy to analyze Chlamydia trachomatis F/SW4 illumina sequence. We could not ...
• Downloading Reference Sequences And Other Questions
  Hi I have a few questions 1. I am trying to use Bowtie to map my data using a reference genome. ...
• Galaxy unable to recognize MAF imported from UCSC genome browser
  Hello all, I have successfully used the "Extract MAF blocks" tool from Galaxy, using the cached ...
• STAR parameters in plants genomes
  Dear all, I want to use the STAR alignment tool available in usegalaxy.org, i know that the defau...
• STAR parameters in plants genomes
  Dear all, I want to use the STAR alignment tool available in usegalaxy.org, i know that the defau...
• Extracting Sequences with coordinates directly from the human genome(hg19), using biopython or Galaxy
  Hi! I am not able to enter the build number in 'Fetch Sequences for intervals in' section in the ...
• NCBI SRA Tool Importer can't import a list
  I am having trouble importing lists of SRA accession numbers using the NCBI SRA Tools. I am using...
• Error Even Starting Up Galaxy
  Hi gang, I've setup galaxy to run before. But this time around, the server will not start. The ...
• genome mappability and peak calling
  I am working with a brassica plant that it is not the model Arabidopsis thaliana. How important i...
• Profile annotation No table available
  Dear all, I have a bed file not annotated, and I would like to use the Operate on genomic interv...
• Need help with "Tophat2" tool - no chicken genome
  Hi, I am new to Galaxy (which is great, thanks!) and I would like to use Tophat2 with chicken da...
• Import Files From Filesystem Path : No Redundance?
  Hi all, I have used the option "Import files from filesystem path" to import a complete arboresce...