Using Sierra with Singleron Biotechnologies Platform

[hkarakurt8742]

Hello everyone,
I am using Sierra for 10X data and it is going perfect but one of my datasets are generated using Singlerin Biotechnologies (scopeV1 chemistry) and it is also 3'-UTR based sequencing method similar to 10X. It also generates similar files such as "barcodes.tsv". The company uses "Celescope" a software for pre-processing (kind of like CellRanger, it uses STAR for alignment). It generates files:

-Sample_Aligned.out.bam
-Sample_cutadapt.json
-Sample_Log.final.out
-Sample_Log.out
-Sample_Log.progress.out
-Sample_SJ.out.tab
-Sample_stat.txt
-barcodes.tsv
-genes.tsv
-matrix.mtx

So basically can I use "Sample_Aligned.out.bam" and barcodes files for Sierra directly or should I do something different?
Also, it it possible to use "SJ.out.tab" instead of regtools output bed file?

Thank you in advance.

[rj-patrick]

Hi @hkarakurt8742,

Yes, use those bam and barcodes files, and yes you can use the SJ.out.tab file in place of the regtools bed file.

Cheers,
Ralph