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Published December 21, 2017 | Version 0.5.2
Software Open

CGATOxford/UMI-tools: 0.5.2

Creators

  • 1. University of Sheffield
  • 2. Yeo Lab
  • 3. Stony Brook University
  • 4. Boston University
  • 5. @bihealth
  • 6. Lund University Cancer Center
  • 7. MRC

Description

  • Adds options to specify a delimiter for a cell barcode or UMI which should be concatenated + options to specify a string splitting the cell barcode or UMI into multiple parts, of which only the first will be used. Note, this options will only work if the barcodes are contained in the BAM tag - if they were appended to the read name using umi_tools extract there is no need for these options. See #217 for motivation:
    • --umi-tag-delimiter=[STRING] = remove the delimeter STRING from the UMI. Defaults to None
    • --umi-tag-split=[STRING] = split UMI by STRING and take only the first portion. Defaults to None
    • --cell-tag-delimiter=[STRING] = remove the delimeter STRING from the cell barcode. Defaults to None
    • --cell-tag-split=[STRING] = split cell barcode by STRING and take only the first portion. Defaults to - to deal with 10X GEMs
  • Reduced memory requirements for count --wide-format-cell-counts: #222
  • Debugs issues with --bc-pattern2: #201, #221
  • Updates documentation: #204, #210, #211 - Thanks @kohlkopf, @hy09 & @cbrueffer

Files

CGATOxford/UMI-tools-0.5.2.zip

Files (22.1 MB)

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Additional details

Related works

Is supplement to
https://github.com/CGATOxford/UMI-tools/tree/0.5.2 (URL)