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Hoohm / CITE-seq-Count

A tool that allows to get UMI counts from a single cell protein assay
https://hoohm.github.io/CITE-seq-Count/
MIT License
79 stars 44 forks source link

Complex whitelist #168

Open alanaleah89 opened 2 years ago

alanaleah89 commented 2 years ago

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 commented 2 years ago

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

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?

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alanaleah89 commented 2 years ago

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.