Hi We are currently seeing a number of methods that are utilising the power of unique molecular indexing. Unfortunately, there is no consensus on how libraries should be configured, and therefore no consensus for how to deal with them within Galaxy.
Often libraries that have the UMI placed directly downstream of the first (i7) index, such as ones using the IDT xGen adapter set (https://www.idtdna.com/pages/products/next-generation-sequencing/adapters/xgen-dual-index-umi-adapters-tech-access). Sometimes UMI's exist in place of the second (i5) index (https://www.neb.com/nebnext-direct/nebnext-direct-for-target-enrichment). In both cases, the recommended workflows are convoluted and all the necessary tools do not currently exist in the toolshed (so that the datasets need to be taken out of galaxy, processed and reloaded). It is possible to use bcl2fastq to output the UMI as an additional fastq file, but this would then require me to create a dataset triplicate (not pair) which afaik we can't do (yet). A quick Google/toolshed search had me find UMI-Tools & Je-Suite which both exist in Galaxy. Both these tools assume the UMI is "in-line" (i.e. at the beginning of the read 1 or read2 - not its own read), extract/remove the UMI and place it in the read header, where it is then used further down the line to dedup the bam file. Does anyone know of any tools that would take the UMI from a separate fastq and use it to tag the headers of actual read data. Or alternatively, a tool that will paste the UMI tag onto the 5' end of the read fastq? And whether these steps can be done within Galaxy, or maybe prior to fastq upload? Anyone have a method/workflow for UMI's? Thanks in advance Tony
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