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• Peak Overlap Analysis, Allowing Space Between "Overlapping" Peaks
  Hello - I have been trying to find a solution to identify overlapping peaks between two ChIP-Seq...
• Need help with "Count intervals in one file overlapping intervals in another file" tool
  Hi, I'm using Galaxy public on a windows computer. The 'Count intervals in one file overlapping ...
• Counting Intervals In One File Overlapping Intervals In Another File - What Are The Hidden Settings?
  Hi, I am using the "Count intervals in one file overlapping intervals in another file" tool (part...
• 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...
• Count intervals in one file overlapping intervals in another file -No longer available?
  Hi,  I have used the 'Count intervals in one file overlapping intervals in another file' tool fr...
• Count intervals of non-uniquely mapped reads overlapping the genome
  Hello everyone, I have some SAM/BAM files containing the alignments of small RNA-seq reads to mm...
• htseq-count not working
  I've been trying to use htseq-count but it is not working. It has been showing "!". Is something ...
• what features are counted by 'compute both depth and breadth'?
  I used the bed tool Compute both depth and breadth of coverage', but it is not clear to me whethe...
• Duplicate row names error with EdgeR on FeatureCounts files
  Hi all, I created tabular count files using FeatureCounts with a GTF file (iGenomes, UCSC hg38) ...
• Re: Strand Info In The Second Query Is Not Recognized By "Interval Intersection"
  The behavior of this tool is intentional. Regardless of which direction a feature is encoded in, ...
• Has the operate on genomic intervals - intersect feature been removed?
  Hello, The intersect tool under "Operate on Genomic Intervals" has suddenly disappeared.  Is thi...