Sam’s Notebook

University of Washington - Fishery Sciences - Roberts Lab

Posts - Page 2 of 113

Data Wrangling - Rename Pgenerosa_v074 Files and Scaffolds

  • ~1 min read

Continuing to organizing files for a manuscript dealing with the geoduck genome assembly/annotation we’ve done, we decided to rename the files as well as rename the scaffolds, to make the naming consistent and a bit easier to read (both for humans and computers).

Read More

Data Wrangling - Splitting BAM by Size for Upload to OSF

  • ~1 min read

We’re in the process of organizing files for a manuscript dealing with the geoduck genome assembly/annotation we’ve done. As part of that, we need the Stringtie BAM file that was used with GenSAS for Pgenerosa_v074 annotation to upload to the Open Science Foundation repository for this project. Unfortunately, at 73GB, the file far exceeds the individual file size limit for OSF (5GB). So, I split it into 5GB chunks. See the following notebook for deets:

Read More