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Published March 9, 2017 | Version 0.3.7
Software Open

CGATOxford/UMI-tools 0.3.7

Creators

  • 1. University of Sheffield
  • 2. Boston University
  • 3. @bihealth
  • 4. MRC

Description

Added functionality:

  • Deduplicating on gene ids ( #44 for motivation): The user can now group/dedup according to the gene which the read aligns to. This is useful for single cell RNA-Seq methods such as e.g CEL-Seq where the position of the read on a transcript may be different for reads generated from the same initial molecule. The following options may be used define the gene_id for each read: --per-gene --gene-transcript-map --gene-tag

  • Working with BAM tags (#73, #76, #89): UMIs can now be extracted from the BAM tags and . See following options for controlling this behaviour: --extract-umi-method --umi-tag --umi-group-tag

  • Ouput unmapped reads (#78) The group command will now output unmapped reads if the --output-unmapped is supplied. These reads will not be assigned to any group.

+ bug fixes for group command (#67, #81) and updated documentation (#77, #79 )

Files

CGATOxford/UMI-tools-0.3.7.zip

Files (12.3 MB)

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Additional details

Related works

Is supplement to
https://github.com/CGATOxford/UMI-tools/tree/0.3.7 (URL)