See post for details.
Project Repository Link
NOTE: Private. Contains unpublished data from collaborators, so the link here and in this post will only work for folks who have been granted collaborative status on the repository until it can be made public later.
grace-ac/project-pycno-multispecies-2023
Alignments
P. helianthoides
Code: 12-hisat2_pycno.Rmd
Output:
Alignment MultiQC Report: pycno_2023_alignment_multiqc_report.html
Alignment Rates:
Exposed, Day 12
| Sample ID | Alignment Rate | Species |
|---|---|---|
| PSC-0519 | 79.18% | P. helianthoides |
| PSC-0525 | 79.40% | P. helianthoides |
| PSC-0531 | 78.52% | P. helianthoides |
| PSC-0537 | 77.72% | P. helianthoides |
| PSC-0549 | 80.91% | P. helianthoides |
| PSC-0561 | 81.66% | P. helianthoides |
23464 genes; 25831 transcripts.
P. ochraceus
Code: 13-hisat2_pisaster.Rmd
Output:
Alignment MultiQC Report: pisaster_2023_alignment_multiqc_report.html
Alignment Rates:
Exposed, Day 12
| Sample ID | Alignment Rate | Species |
|---|---|---|
| PSC-0518 | 86.49% | P. ochraceus |
| PSC-0524 | 85.01% | P. ochraceus |
| PSC-0530 | 85.92% | P. ochraceus |
| PSC-0536 | 85.03% | P. ochraceus |
| PSC-0548 | 86.61% | P. ochraceus |
| PSC-0560 | 83.84% | P. ochraceus |
32370 genes; 35696 transcripts.
D. imbricata
Code: 14-hisat2_derm.Rmd
Output:
Alignment MultiQC Report: dermasterias_2023_alignment_multiqc_report.html
Alignment Rates:
Exposed, Day 12
| Sample ID | Alignment Rate | Species |
|---|---|---|
| PSC-0529 | 87.81% | D. imbricata |
| PSC-0523 | 85.42% | D. imbricata |
| PSC-0529 | 83.73% | D. imbricata |
| PSC-0535 | 88.16% | D. imbricata |
| PSC-0547 | 86.96% | D. imbricata |
| PSC-0559 | 87.01% | D. imbricata |
22124 genes; 25030 transcripts.
Annotations
Each species has a protein annotation of the genome, each one called the same “augustus.hints.aa”. I ran blastp on each of these files to get uniprot/sprot annotation of the genes/transcripts which can then be join-ed with the count matrices for annotation.
P. helianthoides
Code:
- BLAST: 15-BLAST-pycno.Rmd
- Annotation
join-ing: 18-annot-pycno.Rmd
Output:
Ran blastp on the augustus.hints.aa file from https://datadryad.org/dataset/doi:10.5061/dryad.51c59zwfd.
From the BLAST output, the uniprot accession IDs were then put in the ID Mapping feature at uniprot.org, then a big table of GO annotations was downloaded.
That table was join-ed with the Phel_aughintcod_blastout_sep.tab
THEN, I join-ed the P. helianthoides transcript count matrix with the big annotation table, resulting in this annotated transcript count matrix:
output/18-annot-pycno/Phel_transcript_counts_annotation.tab
P. ochraceus
Code:
- BLAST: 16-BLAST-pisaster.Rmd
- Annotation: 19-annot-pisaster.Rmd
Output:
Ran blastp on the augustus.hints.aa file from Mike Dawson and Lauren Schiebelhut (not publicly available yet).
From the BLAST output, the uniprot accession IDs were then put in the ID Mapping feature at uniprot.org, then a big table of GO annotations was downloaded.
That table was join-ed with the Pisaster_aughintcod_blastout_sep.tab.
THEN, I join-ed the P. ochraceus transcript count matrix with the big annotation table, resulting in this annotated transcript count matrix:
output/19-annot-pisaster/Pisaster_transcript_counts_annotation.tab
D. imbricata
Code:
- BLAST: 17-BLAST-derm.Rmd
- Annotation: 20-annot-derm.Rmd
Output:
Ran blastp on the augustus.hints.aa file from from Mike Dawson and Lauren Schiebelhut (not publicly available yet).
From the BLAST output, the uniprot accession IDs were then put in the ID Mapping feature at uniprot.org, then a big table of GO annotations was downloaded.
That table was join-ed with the Dermasterias_aughintcod_blastout_sep.tab.
THEN, I join-ed the D. imbricata transcript count matrix with the big annotation table, resulting in this annotated transcript count matrix: