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Published 20 hours ago • verified publisher icon pachterlab

Rhapsody addition?

Open theheking opened this issue 2 years ago • 3 comments

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

theheking avatar May 04 '22 02:05 theheking

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

Yenaled avatar May 04 '22 03:05 Yenaled

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

colin986 avatar May 17 '23 19:05 colin986

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

sbooeshaghi avatar May 22 '23 18:05 sbooeshaghi