Complex whitelist

[alanaleah89]

I have a complex whitelist, as my scRNA-seq pooled samples were generated using the BD Rhapsody system. Essentially it has a CB region from 0-8, 21-29, 43-51 and UMI position 52-59. The antibody barcode structure is not complex. Is there anyway CITE-seq-Count can be used to help seperate these samples?

[Hoohm]

Hello Alana. The only way that would fit here today is my rewriting R1 and putting all the cell barcodes positions first and then umis last. Then run with the new positions

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On Wed, 4 May 2022, 01:58 Alana Butler, ***@***.***> wrote: I have a complex whitelist, as my scRNA-seq pooled samples were generated using the BD Rhapsody system. Essentially it has a CB region from 0-8, 21-29, 43-51 and UMI position 52-59. The antibody barcode structure is not complex. Is there anyway CITE-seq-Count can be used to help seperate these samples? — Reply to this email directly, view it on GitHub <#168>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAJVO2DFPJNJT7FCXTTWJ5LVIG4RLANCNFSM5VANIG4Q> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[alanaleah89]

Hi Patrick,
Thank you for your reply. However I don't quite understand what you are saying. The cell barcodes are first and umis are last on read1. The read structure for BD Rhapsody is as shown here https://teichlab.github.io/scg_lib_structs/methods_html/BD_Rhapsody.html.
Essentially read1=barcode/UMIs, read2=cDNA/antibody.