gravatar for Kevin Blighe

2 hours ago by

Instigated due to another question: RNA-Seq Cell Barcode Whitelist 10X

I am adding this for the benefit of others, as there is no other resource where the following information is clearly stated, from what I have found.

These are useful for STARsolo parameter configurations when re-aligning 10X Chromium FASTQs.

Table of Contents

10x v1

  • Whitelist, 737K-april-2014_rc.txt
  • CB length, 14
  • UMI start, 15
  • UMI length, 10 (courtesy ATpoint)

10X v2

  • Whitelist, 737K-august-2016.txt
  • CB length, 16
  • UMI start, 17
  • UMI length, 10

10x v3

  • Whitelist, 3M-Feb_2018_V3.txt
  • CB length, 16
  • UMI start, 17
  • UMI length, 12

As per ATpoint, whitelists are available from: github.com/10XGenomics/cellranger/tree/master/lib/python/cellranger/barcodes

These are implemented in STAR as:

  STAR 
    ...
    --soloCBwhitelist [whitelist] 
    --soloCBlen [CB length] 
    --soloUMIstart [UMI start] 
    --soloUMIlen [UMI length] 
    ...

Technically, STARsolo can also be run with --soloCBwhitelist None if no whitelist is provided.

Kevin

link

modified 2 hours ago

written
2 hours ago
by

Kevin Blighe65k



Source link