STARsolo soloMultiMappers cell calling

[Federico Ansaloni]

Hi,

I am running STARsolo enabling the counting of multi--gene UMI (--soloMultiMappers EM). 

I was wondering why the UMI counts calculated considering the multimap are provided only for the raw ("raw/UniqueAndMult-EM.mtx") and not for the filtered cells?

My guess is that the cell calling is performed on the unique UMI only?

If this is the case, is there a specific reason behind that?

Also, what should I do to retrieve the multimap counts for the filtered cells? Is it safe to subset the "raw/UniqueAndMult-EM.mtx" based on the barcode and feature indexes of the "filtered/matrix.mtx" file?

Below the command used is reported.

Thank you.

Regards,

Federico

STAR --runThreadN 40 --genomeDir $dir --readFilesIn $R1 $R2 --readFilesCommand zcat --outFileNamePrefix $name --outSAMtype BAM SortedByCoordinate --outBAMsortingThreadN 40 --quantMode GeneCounts --outTmpDir $tmp --outMultimapperOrder Random --soloType CB_UMI_Simple --soloCBwhitelist $wl --soloCBstart 1 --soloCBlen 16 --soloUMIstart 17 --soloUMIlen 8 --soloStrand Forward --soloFeatures GeneFull_Ex50pAS --soloMultiMappers EM --soloCellFilter EmptyDrops_CR --soloCBmatchWLtype 1MM_multi_Nbase_pseudocounts --clipAdapterType CellRanger4 --soloUMIfiltering MultiGeneUMI_CR --soloUMIdedup 1MM_CR