RAD-seq remove samples from raw data

Hi All! So, I need some help getting off the ground :sweat_smile:

I sent in a plate of 96 samples for RAD-seq: Half were my samples, half were a colleague’s. However, the company returned a single file of all sequences produced in fastqsanger format, including both mine and my colleague’s samples intermixed together.

Does anyone know how to filter this so I that only analyze my own samples?
I tried “Filter Fasta” already, but this failed.

All the sequences are in a single interleaved fastq file? Did they provide a sample sheet? You would need that to separate your own samples, too.

Hi jennaj,

Yes, the sequence reads all came back as an interleaved fastq file. They provided a sample sheet so I know which samples are mine and which are not, so my problem is purely a logistical one in figuring out how I select for my own samples!

However, having talked to a few people, it seems my only option is the demultiplex all of the sequences first and then select which sequences I want to use in downstream analyses. If you have another idea, though, I’d love to hear it!

This sounds correct to me, too. https://training.galaxyproject.org/