search

nf-core / airrflow

B-cell and T-cell Adaptive Immune Receptor Repertoire (AIRR) sequencing analysis pipeline using the Immcantation framework
https://nf-co.re/airrflow
MIT License
52 stars 34 forks source link

Analyzing BCR Rep-Seq Data in nf-core/airrflow Without Primer Information #277

Closed pengjiao closed 11 months ago

pengjiao commented 1 year ago

Description of feature

Hello,

I'm working with BCR Rep-Seq data and I have the resulting FASTQ files along with UMI information. However, I do not have the primer information for my samples. Would you have any recommendations or suggestions on how I can proceed with the data analysis using the nf-core/airrflow pipeline without the primer details? Any guidance would be greatly appreciated.

Thank you in advance!

ggabernet commented 11 months ago

Hi @pengjiao , yes indeed the BCR Rep-seq data requires knowing the primer information for processing unfortunately. Sometimes it is possible to guess the primers by doing a sequence alignment of the reads, for example with ClustalW

ggabernet commented 11 months ago

I will close this issue, but if you have further questions on how to find the primers you can continue asking here. We also have a slack channel that can be more useful for this kind of discussions: https://nf-co.re/join