COMBINE-lab/salmon

Salmon alevin errors out when cell barcode length is > 31 base pairs

Opened this issue · 1 comments

tl;dr

  • salmon alevin returns an error if the cell barcode length is > 31 base pairs
  • This blocks me from using salmon alevin for a novel scRNA-seq chemistry that has a 34 base pair cell barcode.
  • Previously the salmon alevin maximum cell barcode length was increased from 20 base pairs to 31 base pairs. #629
  • Could you please increase the maximum cell barcode length again?
    • Or provide guidance on how I should do this in my own fork of salmon?

Summary

This bug primarily related to alevin (single-cell mode).

Describe the bug

To Reproduce

salmon alevin
    -i /path/to/salmon_index 
    -p 16 
     -l ISR
    --read-geometry 2[1-100]        
    --bc-geometry 1[1-34]         
    --umi-geometry 1[35-44]         
    --sketch         
    -1 /path/to/r1.fastq 
    -2 /path/to/r2.fastqs
    -o /output/path        
     --tgMap /path/to/t2g.tsv

Steps and data to reproduce the behavior:

Specifically, please provide at least the following information:

Expected behavior
Salmon alevin does not error out when the cell barcode length is 34 base pairs.

Screenshots
Error log
[2024-06-17 22:00:25.466] [alevinLog] [error] Barcode length (34) was not in the required length range [1, 31].

Desktop (please complete the following information):

  • OS: Ubuntu 22.04

Following up on this, if I was to fork salmon and fix this, would the correct solution be to update the following line?

uint32_t maxBC{31};