Posts
DNA Isolation - C.gigas Ploidy Experiment Ctenidia
Isolated DNA from the remaining ctenidia tissue samples from Ronit’s experiment (Google Sheet).
Annotation - Geoduck Genome with MAKER Submitted to Mox
Well, here we go! Initiating full-blown annotation of the Pgenerosa_v070 (FastA; 2.1GB), using MAKER (v.2.31.10) on Mox. This will perform the following:
Annotation - Olurida_v081 MAKER Functional Annotations on Mox
Believe it or not, full, proper annotation of the Olympia oyster genome is nearly complete! Here’s where it stands:
Annotation - Olurida_v081 MAKER Proteins BLASTp on Mox
After getting through the initial MAKER annotation and SNAP gene predictions, and then renaming the sequences, I needed to run BLASTp on the FastA file produced by MAKER id mapping in order to assign functionality to the predicted genes.
Annotation - Olurida_v081 MAKER Proteins InterProScan5 on Mox
Continuation of genome annotation of the Olympia oyster genome. Determined initial gene models using MAKER with two rounds of SNAP, relabeled with more user-friendly names, and then performed protein-level annotations using BLASTp. Next, I’m going to run InterProScan5 (IPS5) to help functionally characterize the O.lurida proteins ID’d by MAKER. Once this is complete, I’ll use MAKER to incorporate the IPS5 and BLASTp results into a much more neatly (i.e. human-readable) annotated genome!
Annotation - Olurida_v081 MAKER ID Mapping
After getting through the initial MAKER annotation and SNAP gene predictions, I needed (wanted?) to simplify annotation names that will be easier to read and are in a more standardized format; similiar to NCBI.
Gene Prediction - HiSeqX Metagenomics from Geoduck Water Using MetaGeneMark on Mox
After assembline the metagenomic data yesterday, I needed to predict some genes. I did this using MetaGeneMark (v.3.38) and ran it on Mox.
Metagenome Assembly - P.generosa Water Sample Trimmed HiSeqX Data Using Megahit on Mox
Attempting an assembly of our geoduck metagenomics HiSeqX data using Megahit (v.1.1.4) on a Mox node.
VCF Splitting - C.virginica VCF Using BCFtools
DNA Isolation - C.gigas Ploidy Experiment Ctenidia
Yesterday, Ronit initiated DNA isolation from ctenidia samples from his experiment (Google Sheet) from the following four samples: