In bisulfite mode, run Bismark using local alignments
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FelixKrueger commented
To avoid having to run FastQ Screen on trimmed FastQ files in --bisulfite mode, could you please allow Bismark to be run using local alignments (flag: --local), similar to what you are doing already for Bowtie2 and BWA?
StevenWingett commented
We looked at the effect of making the Bismark option --local the default by processing the Bismark Test Dataset (results attached). This resulted in a large number of extra reads now categorised as multi-mapping. This was considered excessive. Consequently, instead of making --local the Bismark default, FastQ Screen now has a new --bismark option to which Bismark parameters may be passed (for example --bismark "--local" maps with Bismark in local mode.
Commit: aaac84a