Salmon alevin errors out when cell barcode length is > 31 base pairs
Opened this issue · 1 comments
connersk commented
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:
- Salmon version
v1.10.1
- How was salmon installed? -> Compiled
- Encountered this error when running a feature barcoding analysis following this tutorial https://combine-lab.github.io/alevin-fry-tutorials/2021/af-feature-bc/
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