Extract barcodes (sample and UMI) from read names

pachterlab / splitcode

Flexible and efficient parsing, interpreting and editing of sequencing reads

https://pachterlab.github.io/splitcode/

BSD 2-Clause "Simplified" License

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Extract barcodes (sample and UMI) from read names #22

Open nh13 opened 1 month ago

nh13 commented 1 month ago

In some cases, we get FASTQs that have sample barcodes and UMIs in the read name and I we'd like to extract those. Is that possible?

See: [1] https://help.basespace.illumina.com/files-used-by-basespace/fastq-files [2] https://knowledge.illumina.com/software/general/software-general-reference_material-list/000002211

Yenaled commented 1 month ago

This feature is not available yet. I'm working on some major upgrades to splitcode this month, and I'll be sure to add this in in the next week or two.