See post for details on the multispecies count matrices developed using hisat2 and stringtie.

Overview

REMINDER: GitHub repo is private due to use of data from collaborators that are not published yet, so the links to code and data files will only work for current project collaborators

For each species, I have 24 libraries: controls, n=6 Day 6, n=6 Day 12; exposed, n=6 Day 6, n=6 Day 12.

Each one has a genome ( P. helianthoides genome is publicly available (Schiebelhut et al., 2023); P. ochraceus and D. imbricata are not).

The libraries were first trimmed (see post: Multi-Species - Day 6 and Day 12 RNAseq data FastQC and Trimming).

Then, the trimmed RNAseq libraries were aligned to their genomes using hisat2 and stringtie and then count matrices were created (both for genes and transcripts).

P. helianthoides

Code: project-pycno-multispecies-2023/code/26-hisat2-pycno-d6-d12.Rmd)

Aligment MultiQC Report on OWL: gcrandall/multispeciesSSWD/QCreports/pycno_2023_alignment_ALL_multiqc_report.html

Gene count matrix:
project-pycno-multispecies-2023/data/pycno_gene_count_matrix_2023.csv

Transcript count matrix:
project-pycno-multispecies-2023/data/pycno_transcript_count_matrix_2023.csv

P. ochraceus

Code: project-pycno-multispecies-2023/code/27-hisat2-pisaster-d6-d12.Rmd)

Alignment MultiQC Report on OWL:
gcrandall/multispeciesSSWD/QCreports/pisaster_2023_alignment_ALL_multiqc_report.html

Gene count matrix:
project-pycno-multispecies-2023/data/pisaster_gene_count_matrix_2023_all.csv

Transcript count matrix:
project-pycno-multispecies-2023/data/pisaster_transcript_count_matrix_2023_all.csv

D. imbricata

Code: project-pycno-multispecies-2023/code/28-hisat2-derm-d6-d12.Rmd

Alignment MultiQC Report on OWL:
gcrandall/multispeciesSSWD/QCreports/derm_2023_alignment_ALL_multiqc_report.html

Gene count matrix:
project-pycno-multispecies-2023/data/derm_gene_count_matrix_2023.csv

Transcript count matrix:
project-pycno-multispecies-2023/data/derm_transcript_count_matrix_2023.csv