STARsolo velocity counts computation in SmartSeq2

[okko...@gmail.com]

Hi,

I tried using velocity for counts output with STARsolo on SmartSeq2 data, here's my command:

TOOL=/home/okonechn/tools/STAR-2.7.9a/bin/Linux_x86_64/STAR

$TOOL --genomeDir $GENOME --readFilesCommand zcat --runThreadN 8 --outFilterMultimapNmax 1  --outSAMtype BAM SortedByCoordinate  --soloType SmartSeq --readFilesManifest manifest_16161.cfg --soloUMIdedup Exact --soloStrand Unstranded --soloFeatures Gene Velocyto

Then error occurred: 

"--soloFeatures Velocyto is presently not compatible with --soloType SmartSeq".

Is it going to be updated? Or did I miss anything? Actually, SmartSeq data is technically more suitable for velocity computation in comparison to 10X and other 5'/ 3' protocols, so it would be great to have this option. Can also create an issue in git repo if it would be useful.

Best regards,

   Konstantin 

[Alexander Dobin]

Hi Konstantin,

this feature is not available yet, unfortunately.

I am getting a number of requests for it, so it's high on my priority list.

I hope to complete it within 1 month.

Cheers

Alex