Exon capture with ref, popgen projects - CGRL-QB3-UCBerkeley/seqCapture GitHub Wiki

Introduction:

Probe design:

Exon captures can be always easily designed using a pre-existing reference genome for population genetic projects. Probe design is usually conducted by a bioinformatics team by the vendor. Because a reference genome is companioned with gff/gtf, selection of exons for each gene can relatively be an easy task. Soft repeat masking is also done by the bioinformatician though I recommend researchers to conduct hard masking (if not done already) before submitting the reference and gtf/gff to the vendor for probe design.

Nevertheless, if a pre-existing reference is used for probe design, then running this step is not needed for population genetic project. Please move forward with Step 4: "Aligning reads"