Hey everyone, I have been working with single cell long read data for a while now and came across your pipeline. Love the idea of a reproducible pipeline. I was wondering if there is a plan to implement 10X_5v3 as barcode option or can you also input custom barcode/umi length? They only made the UMIs 2 bp longer and use a new whitelist, so the changes are quite small. Cheers, Jonas

Hi Jonas - thanks for your interest in scnanoseq. Yes! We plan on upgrading blaze in version 1.2.0 which supports more 10X Kit versions ('3v4', '3v3'(default), '3v2', '3v1' for 10X 3' GEX kit v4 to v2 respectively, and '5v3', '5v2' for 10X 5' GEX kit v3 and v2). As for the whitelist, the current pipeline has the defaults we present but also accept any custom whiltelist as well. That being said, before 1.2.0 we are trying to get 1.1.0 out along with a preprint to present scnanoseq to a broader audience (and metrics). But we hope we can push a BLAZE upgrade sometime this semester hopefully. @Austyn Trull: any other thoughts?

I think that about covers it, the BLAZE upgrade is our next priority after this 1.1.0 release. We can also let you know when it gets put into the

dev

branch so you can begin testing it a little ahead of release

Hey thanks for your replies. Sounds good. Happy to give it a try in the dev branch. I currently use SiCeLoRe2.1+Isosceles. Definitely interested to run a comparison.

Hi @Jonas Berger, we’ve got the BLAZE upgrade in our

dev

branch. If you want to give it a try you should just need to do the following: 1. If you’ve previously downloaded/ran scnanoseq, run the below command. Otherwise, go to step 2.

nextflow pull nf-core/scnanoseq

2. I’ve provided an example command below, update as needed for your dataset and files. The important thing is to include the

-r dev

as this will use the

dev

version of scnanoseq

nextflow run nf-core/scnanoseq \
    -r dev \
    --outdir ./results \
    -params-file ./params.yml \
    -c ./custom.conf

The full list of kits supported by the

barcode_format

parameter in dev are: • 10X_3v4 • 10X_3v3 • 10X_5v3 • 10X_5v2 One thing to note is we don’t currently have any test data for the new barcode kits, so we haven’t been able to do any good tests as of yet. So be sure to let us know if you encounter any issues while using them, and we’ll be happy to resolve them the best we can!

Cool, I will give it a try!

Hi @Jonas Berger, Just wanted to check in if you’ve had a chance to try the new version of BLAZE yet? We’re preparing to go ahead and release the new version as we’ve got other changes and fixes that we want to go ahead and put out there. We’ll of course fix any bugs after release, but wanted to check in since you had mentioned wanting to try the new updates. If you haven’t that’s okay as well, just wanted to check so we can plan accordingly

Hi @Austyn Trull, I have some 10X_3v4 data from our lab and tried the dev branch. It worked for me!

Hi @Austyn Trull, Sorry for not getting on this earlier. I had some problems with our cluster. I have tried the 10X_5v3 option and it works for me. Thanks!