Here’s where things stand for Summer 2021 and Summer 2022 analyses.

Notes:

Per Steven’s suggestion, I made a wiki in my GitHub repo describing the key data files and providing information about where they live:

GitHub repo: grace-ac/paper-pycno-sswd-2021-2022
Wiki Page in repo: here

BLAST the P. helianthoides genome gene list (actually transcripts) to get annotation

Goal –> annotate the genome with BLAST annotation to later annotate the DEG lists.

Code: paper-pycno-sswd-2021-2022/code/16-blast-annotation.Rmd

BLAST output:
paper-pycno-sswd-2021-2022/analyses/16-blast-annotation/blast_out.tab

kallisto alignment

paper-pycno-sswd-2021-2022/code/17-kallisto-2021-2022.Rmd

Count matrix:
paper-pycno-sswd-2021-2022/data/2021-2022_kallisto_count_matrix_rounded_20240918.tab

DESeq2 to get DEG lists:

paper-pycno-sswd-2021-2022/code/18-deseq2_2021_2022.Rmd

DEG lists:

Summer 2021

8 control adults vs 8 exposed adults:
paper-pycno-sswd-2021-2022/data/expB_DEG_DET_lists/DEGlist_8v8_2021_exposedVcontrol.tab

Annotated DEG list with counts and BLAST paper-pycno-sswd-2021-2022/data/expB_DEG_DET_lists/DEGlist_8v8_2021_exposedVcontrol_counts_BLAST.tab

Summer 2022

Exposed V Control taking age into account:

DEG list:
paper-pycno-sswd-2021-2022/data/2022_DEG_DET_lists/DEGlist_2022_exposed_v_control_no_contrast.tab

Annotated DEG list with counts and BLAST:
paper-pycno-sswd-2021-2022/data/2022_DEG_DET_lists/DEGlist_2022_noage_contrast_counts_BLAST.tab

Exposed V Control taking age into account, contrasting age to get the DEGs that are different by age group:

DEG list:
paper-pycno-sswd-2021-2022/data/2022_DEG_DET_lists/DEGlist_2022-contrast_age.tab

Annotated DEG list with counts and BLAST:
paper-pycno-sswd-2021-2022/data/2022_DEG_DET_lists/DEGlist_2022_agecontrast_counts_BLAST.tab