alexdobin
commented
10 months ago Hi @wjy123009
This configuration looks similar to 10X 5' protocol, so your parameters might be similar to these: https://github.com/alexdobin/STAR/blob/master/docs/STARsolo.md#barcode-and-cdna-on-the-same-mate
I'm trying to use STARsolo to analyze novel scRNAseq data using techniques such as scFAST-seq or snRandom-seq. The principle is basically the same, using random primers to capture single cells. Its paired-end 150bp sequencing data structure is as follows: Read1:17bp CB+12bp UMI+cDNA Read2:10XTSO sequence+cDNA.
It can be seen that both fastq contain a lot of cDNA information. If it uses double-end comparison, it will definitely be able to obtain new mutations or SJ and other information.
However, the current STAR-solo pipeline mainly uses single-end comparison, and the --soloType CB_samTagOut module does not use UMI counting and adding UB, UR and other related content. I wonder if UMI can be added in subsequent updates.
Even better is to enter an additional parameter when using the CB_UMI_Simple module, such as double mate comparison, etc.
looking forward to your reply.
Cheers junyangWu