CGATOxford/UMI-tools 0.3.7

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