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• Liftover tool not working at UCSC
  Hello, I tried to convert hg18 coordinates in a BED format data with UCSC liftover and it is not...
• Blast
  Hi... I have an analysis of 18,000,000 + sequences (X4) blasting through the HTGS database. Is ...
• Convert genome coordinates between assemblies and genomes (Galaxy Version 1.0.5) aka LiftOver
  I have two related bacterial genomes of same species - different subspecies. I want to map the co...
• Problem Report!!
  Dear Galaxy member, I'm sending you this e-mail because of a problem I have in fetching sequence...
• Can you use Galaxy Lift-over to convert ce10 genome coordinates to ce11?
  I am trying to convert wig (or bigwig) and bed (or bigbed) files from the UCSC ce11 (WBcel235) co...
• Using Lift-Over to convert GRCh37 to GRCh38. "no option available" for converting "To" field
  I have a bed file in GRCh37 coordinates that I want to convert to GRCh38. I am trying to use li...
• Naming Maf Blocks
  Dear all, I heve done this in steps: 1. Go to genome.ucsc.edu and select the tables link. 2. Sel...
• Need help with "Convert genome coordinates" tool
  I would like to convert a bed file from mm10 to mm9, but I don't see mm9 as an option in the pull...
• Lift-Over tool in Galaxy error: 'Exception caught attempting conversion: '
  Dear all, I'm trying to remap mm9 genome coordinates to mm10 from a .BED file. Galaxy "Lift-Ove...
• Convert genome coordinates from hg38 to hg19
  I think I have done this before and it worked perfectly, a few weeks ago, but somehow I can't get...
• Extract Genomic DNA using coordinates from a gff file
  Hi, I have been extracting genomic sequences, using "Extract genomic DNA" from "Fetch Alignment...
• susScr11 not available for liftover ?
  Hi, I wanted to covert mm10 coordinates to susScr11 using the LiftOver tool, but the latest assem...
• Galaxy interval format - what should be provided as CHROM#?
  Dear colleagues, I have a .txt file with >100 lines of the following format (1st column - seq...
• Contig assembly on MicrobesNG data
  Hello, I recently had the genome of the bacteria that I am working on sequenced by MicrobesNG. T...
• Can't filter unmapped reads in my BAM file
  Hello everyone. I'm a newbie in bioinformatics and I'm trying to filter a BAM file using the Gala...
• Cufflinks tool locally cached 'hg38' malformed; error reads: 'An invalid option was selected for index, u'hg38', please verify'
  Greetings, I am trying to use the Cufflinks tool in the main/public instance of Galaxy to gen...
• Builtin genome in Galaxy is not displayed in IGB
  Hi, I mapped my peak using MACS in Galaxy using the built-in genome. I can visualize my peaks in...