STARsolo
you can concatenate the files, or supply them as two (for Read2(barcode) and Read1(cDNA)) comma-separated lists, i.e.
Hi Olga,
I have finally finished implementation of single-cell BAM tags output, to make STARsolo BAM output similar to CellRanger and compatible with downstream tools such as velocyto.
It's released as a branch for now:
https://github.com/alexdobin/STAR/tree/soloDevelop
The implemented tags are: CR UR CB UB GX GN
Example run command
STAR ... --readFilesIn Read_cDNA.fastq Read_barcode.fastq --soloType Droplet --soloCBwhitelist /path/to/737K-august-2016.txt --soloFeatures Gene --outSAMtype BAM SortedByCoordinate --outSAMattributes NH HI CR UR CB UB GX GN
If you are still interested in testing it, please let me know how it goes.
Cheers
Alex
