It is not recommended to use TI with V3 chemistry run, if you want to use TI-like workflows to analyze data we recommend you use the latest Mosaic v3.0 library.
The V3 loom files may be used with TI 2.2 but you may see the following 2 issues:
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- V3 runs have a higher cell capture rate with ~15k cells on average, this large volume of cells and related variant data can cause your computer to run out of memory.
- The low coverage cells from V3 adds to missing variant data that affects the two cell based filters namely - minimum percentage of cells with variant and minimum percentage of cells with mutated variant.
Therefore, it is recommended that Mosaic v3.0 is used with V3 data, but in case you want to use TI here are a few suggestions:
- If the variants of interest are present in the filtered variants (sample is loaded with filter_variants=True in Mosaic) then load the data with intersected cells(filter_cells=True) and convert that to the loom file and load it in insights.
- If you have enough memory, you can load all the variants (sample is loaded with filter_variants=False in Mosaic), filter them until you have the desired set and export to a loom file.
- If you only have a few samples - then you can reduce the variant thresholds in Insights itself until you find the variants you are interested in and analyze that data - the missing data cells will be discarded and therefore the ideal thresholds for %genotyped cells and %mutated cells will be lower in the variant selection. Subclone generation will be minimally affected - there will be some extra cells and increase in the expected ADO rate.