Demultiplexing Custom Barcodes

Question

[meetmet]

Hey!

I am struggling to find up-to-date software for demultiplexing FASTQ files from RNA-seq data. The FASTQ files have already been demultiplexed by patient using sample barcodes, but they need to be demultiplexed a second time for different conditions. The barcodes are 25 bp long and encode five different conditions for each patient.

I was using the je-utils demultiplexing tool, but it is now outdated, and I’m wondering if anyone knows of newer tools for the same process, with better performance?

Cheers,

[GenoMax]

The barcodes are 25 bp long and encode five different conditions for each patient.

What is the location of these in the data you have? Are they consistently in-line in sequence at a certain location (front of reads?).

sabre is one potential option: https://github.com/najoshi/sabre

[meetmet]

Thank you for your response.

I have paired-end (PE) FASTQ files, and the barcode is located in Read 1, where the sequence contains the entire barcode for a given condition. (Read 1 = 25 bp).

I will try sabre also!