Sam’s Notebook

University of Washington - Fishery Sciences - Roberts Lab

Posts - Page 2 of 133

Transcriptome Comparisons - C.bairdi Transcriptomes Evaluations with DETONATE rsem-eval on Mox

  • 5 min read

UPDATE: I’ll lead in with the fact that this failed with an error message that I can’t figure out. This will save the reader some time. I’ve posted the problem as an Issue on the DETONATE GitHub repo, however it’s clear that this software is no longer maintained, as the repo hasn’t been updated in >3yrs; even lacking responses to Issues that are that old.

Read More

Alignments - C.bairdi RNAseq Transcriptome Alignments Using Bowtie2 on Mox

  • 5 min read

I had previously attempted to compare all of our C.bairdi transcriptome assemblies using DETONATE on 20200601, but, due to hitting time limits on Mox, failed to successfully get the analysis to complete. I realized that the limiting factor was performing FastQ alignments, so I decided to run this step independently to see if I could at least get that step resolved. DETONATE (rsem-eval) will accept BAM files as input, so I’m hoping I can power through this alignment step and then provided DETONATE (rsem-eval) with the BAM files.

Read More