NOTE: This website is largely archived and should be used with caution. It was part of dissertation research, and thus the pipeline and tools may have changed. Keeping the site fully up-to-date is not possible at the current time. Thanks.

Welcome to a RADSeq/RAPTURE pipeline. This website was largely a working lab notebook as part of a dissertation, but provides much of the protocols, pipeline, and code used in RADSeq population genomic analyses. A summary of what is on this site is as follows:

  • Background tab has has info on coding using bash, how to connect to the cluster and to sftp as well as some additional R coding resources.

  • Downloading Data provides info on how to get your data, split by plate, split by barcode, and add metadata.

  • Alignment describes the main ways data will be aligned, (either de novo or reference. There is also a page on merging multiple lanes of data.

  • Filtering shows how to filter data for quality and number of reads. The subsample script will select all bams with reads above a given threshold, and then randomly subsample to exactly that threshold of reads (e.g., so all samples have exactly 100k reads).

  • PopGen Analysis shows a very simplistic set of analyses that can be done using angsd.

  • Colony provides a short pipeline on using Colony with RADSeq data.

  • NCBI describes how to upload data to NCBI for archival purposes.

SF Eel - Elder Ck