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VCCRI / Sierra

Discover differential transcript usage from polyA-captured single cell RNA-seq data
GNU General Public License v3.0
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Using Sierra with Singleron Biotechnologies Platform #64

Closed hkarakurt8742 closed 1 year ago

hkarakurt8742 commented 1 year ago

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 commented 1 year ago

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