I have hisat2 and deseq2 results from sea star coelomcyte RNAseq data from 2021 and 2022 datasets. I want to get gene annotations. See post for details.

Annotating Count Matrices with Gene IDs

R Code: paper-pycno-sswd-2021-2022/blob/main/code/19-get-gene-annotations.Rmd

Gene list IDs pulled from augustus.hints.gtf:
paper-pycno-sswd-2021-2022/data/gene_annotation.tab

Graces-MacBook-Air-10:data graciecrandall$ head -5 gene_annotation.tab
pycn_heli.0392	AUGUSTUS	gene	1	4781	0.95	+	.	g1
pycn_heli.0392	AUGUSTUS	gene	16379	16612	0.78	-	.	g2
pycn_heli.0392	AUGUSTUS	gene	16805	17239	0.97	-	.	g3
pycn_heli.0392	AUGUSTUS	gene	17793	17996	1	-	.	g4
pycn_heli.0069	AUGUSTUS	gene	1394	26872	0.76	-	.	g5

This file will be join-ed with DESeq2 output from analyses using the gene count matrix created in this R code: https://github.com/grace-ac/paper-pycno-sswd-2021-2022/code/20-hisat2-genecount-matrices.Rmd

More to come!