Rhapsody addition?

[theheking]

Hi,
I would love to be able to utilise kallisto bustools to BD Rhapsody single cell analysis however, it is not included in kb --list for technologies. Is there a workaround of entering custom barcode, whitelist, umi and read file information.
Thank you in advance

[Yenaled]

It should be in the technologies list (BDWTA). Perhaps update your version of kb

[colin986]

Hi,

I was wondering if the -x BDWTA option is compatible with the new version of the Rhapsody Assay with the “enhanced beads”. The linkers between the 9 nt cell label sequences have been shortened to 4nt and there is now a variable sequence at the 5’ end of the read which can be either 0,1,2,3 or 4nt

https://teichlab.github.io/scg_lib_structs/methods_html/BD_Rhapsody.html

Thanks,
Colin

[sbooeshaghi]

Hi Colin,

Thanks for reaching out. To facilitate adding the new Rhapsody Assay to kallisto bustools it would be useful if you could create a seqspec specification (please see this GitHub repo with information on how to do that) and provide a small set of reads (1 million is usually small enough to fit on GitHub).

With those two things we can ensure that kallisto bustools is compatible.

Thank you!
Regards,
Sina B