bustools for Parse bio

[David A Knowles]

Hi all - I'm curious if anyone has used bustools for Parse bio scRNA-seq? I see there is now an option in bustools for SPLiT-seq which Parse's tech is developed from. Does the same BC/UMI specification apply? It's difficult to get detailed info from their website. 

Second and related question: SPLiT-seq has its BC split across multiple positions in the second fastq, which is specified in the code as: 

        busopt.nfiles= 2;
        busopt.seq.push_back(BUSOptionSubstr(0,0,0)); 
        busopt.umi.push_back(BUSOptionSubstr(1,0,10)); 

        busopt.bc.push_back(BUSOptionSubstr(1,10,18));
        busopt.bc.push_back(BUSOptionSubstr(1,48,56));
        busopt.bc.push_back(BUSOptionSubstr(1,78,86));

It's not documented, but from my skimming the code in main.cpp I think these multiple BC segments could be manually specified as -x 1,10,18,1,48,56,1,78,86:1,0,10:0,0,0. Is that correct? 

Thanks for all the work on these tools! 

David

[Delaney Sullivan]

Yes, that is correct! I've been using that exact string myself for split-seq data that I have.

[Delaney Sullivan]

And to clarify, by split-seq I mean ParseBio. So yes, that's the correct string to use for ParseBio

[David Knowles]

Thanks! Seems to be roughly working although I get a lot of barcodes with very few counts (median of 1!). Will try with `bustools whitelist` -> `bustools correct` to see if that cleans things up.