Posts
Data Wrangling - Additional Features Stats for Panopea-generosa-v1.0
Although I’d previously generated some feature stats for this genome annotation (see 20191029), we decided we wanted to get some additional info, similar to that of Table 1 in M.Aranda et al 2016. Scientific Reports.
Data Wrangling - Rename Pgenerosa_v074 Files and Scaffolds
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).
Data Wrangling - Splitting BAM by Size for Upload to OSF
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:
Samples Received - Marinelli Shellfish Company C.gigas and C.sikamea Oysters
Steven was recently contacted by Marinelli Shellfish Company to see if we could help them determine if some oysters they had were Crassostrea gigas (Pacific oyster) or Crassostrea sikamea (Kumamoto). Steven knows of a paper with primer sequences to use with qPCR for this specific determination.
Data Wrangling - Create Panopea-generosa-vv0.74.a4 Intron and Intergenic BED Files
Since generating an updated Pgenerosa_v074 annotation, we also needed updated intergenic and intron bed files to put in the OSF repository for this project.
Genome Feature Counts - Panopea-generosa-vv0.74.a4
In preparation for a paper we’re writing, we needed some summary stats for Panopea-generosa-vv0.74.a4. This info will be compiled in to a table for the manuscript. See our Genomic Resources wiki for more info on GFFs:
FastQC-MultiQC - C.bairdi RNAseq Day 12 26 Infected Uninfected
After receiving the rest of the crab data and concatenating it all together, I ran FastQC and MultiQC on the FastQ files.
Data Received - C.bairdi RNAseq Day9-12-26 Infected-Uninfected
Previously, we “received” this data, but it turns out it was incomplete (see 20191003).
Lab Maintenance - Cluster UPS Battery Replacement
Replaced the batteries on one of the APC uninterruptable power supplies (UPS) on our local server cabinet.