Analysis Notebook

PCA for gene count comparison between NCBI Crassostrea gigas Annotation Release 101 and GCF_963853765.1-RS_2024_06 reference genomes

Posted on December 23, 2024 Written by: Steve Yost

12-23-2024 [Read More]

Tags: rnaseq pca

Compare genes after CGI id conversion attempt 1

Posted on December 13, 2024 Written by: Shelly Wanamaker

In order to get 1:1 matching between genes in Roberto’s gene counts matrix and Emma’s gene counts matrix, they need to be the same type of identifier. Most genes in Emma’s are “LOC” and Roberto’s are “CGI” [Read More]

Tags: name-conversion identifiers genome-versions

Exploring nf-core differential abundance workflow

Posted on December 11, 2024 Written by: Emma Strand

We want to test out this nf-core workflow: https://github.com/nf-core/differentialabundance for our RNAseq data output. [Read More]

Tags: nextflow Klone differential-abundance

Re-run FetchNGS for Cvirg_Perkinsus_RNAseq

Posted on December 5, 2024 Written by: Shelly Wanamaker

I realized I made a couple mistakes in getting the data downloaded for the Perkinsus RNAseq reanalysis. [Read More]

Tags: nextflow Klone FetchNGS Perkinsus Dermo

Repoint nf-core projectDir to srlab directory

Posted on December 3, 2024 Written by: Shelly Wanamaker

Purpose The purpose of this post is to describe how to redirect the projectDir when running an nf-core pipeline on Klone. This came up when I attempted to run the methylseq pipeline for the first time and got a disk quota exceeded error (https://github.com/RobertsLab/resources/issues/2045). This happened because nextflow was trying... [Read More]

Tags: nextflow nf-core klone