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• How do I obtain uniquely mappable reads from bowtie on galaxy?
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• bedTools - Genome file
  Hi Galaxy Community, The bedTools tools were updated recently with some great additions. Some of...
• Need help with "Count intervals in one file overlapping intervals in another file" tool
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• Genome file for Bam to Bed or Genome Coverage
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• A question of concept?
  Hi all! I'm new to this so, pardon my noobness. If I were to convert the transcript annotations...
• Bedtools Error
  Hello! I'm using BedTools on the main Galaxy server. I try to use multiinter function to compare...
• Partial alignment statistics
  Hello,   I started using Galaxy some two weeks ago. I am not bioinformatician by training, but ...
• Bedtools coverage not accepting file b
  Bedtools coverage does not accept the -b files. Compute both the depth and breadth of coverage o...
• Downloading tools from toolshed
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• Get fasta file from peak called BED file to do Motif analysis
  Hi all, I have some called peaks in BED format and would like to extract the sequences in a FAST...
• Galaxy: Genomic Intervals to strict BED Conversion
  Hello: I'm new to the forum and Galaxy/bioinformatics. In the last two months I've been followi...
• Counting Rna-Seq Reads Per Class.
  Hi All, I have been trying to count the number of RNA-seq reads that fall into the various Cuffli...