#Acartia tonsa reciprocal transplant
This repository hold scripts for the analysis of a reciprocal transplant of Acartia tonsa following a ~20 generation selection experiment.
These RNAseq data were sequenced on 2 lanes of a Novaseq by Novogene. Data were received by us on 2018-07-24.
Raw sequence data is available at NCBI BioProject PRJNA555881
Gene expression data are included in this repository in DGE_data/
, both normalized (by librarysize) and not normalized.
All other summaries etc. are included as supplemental files with the manuscript.
Please get in touch about any data issues.
Below are scripts to run the full analysis for the manuscript. A short description accompanies each.
- Check data quality:
01_fastqc.sh
- Trim fastq files:
02_trim_AAAA.sh
;02_trim_HHHH.sh
;02_trim_HHAA.sh
;02_trim_AAHH.sh
- Re-run fastqc:
03_fastqc_posttrim.sh
- create index for salmon:
04_salmon_index.sh
- Quantify each sample:
05_salmon.sh
- Generate supertranscript reference to align:
06_supertranscript.sh
- Align to the supertranscript:
07_align.sh
- call variants using varscan:
08_varscan_all.sh
- note that this is very liberal in the calls. Need to filter.
- Filter variants from varscan:
09_filter_variants.R
- calulate pi and look at the loss:
10a_popoolation.sh
,10b_popoolation_pi.R
- run the DAPC:
11_dapc.R
- Run the CMH, output allele freq changes:
12_snp_analysis.R
- Generate the correlation scatter plot for DGE and AF for the supplemental:
13_scatter_plot.R
- GO analysis
- formatted output for DGE is from
13_scatter_plot.R
: "~/reciprocal_t/analysis/GO_enrich/dge_f1.txt" 14b_go_assign_snps.py
,14b_go_assign_dge.py
producesdge_F1_GOterms.out
snp_GOterms.out
, for each generation.14c_GO_format.sh
there are some weird formatting issues (some quotes?) that were just easier to fix with bash14d_GO_Enrich.R
and14d_GO_Enrich_SNP.R
run the actual GO enrichment for expression and snps, respectively14e_go_enrich_deltapi.md
run go enrichment for the change in pi
- formatted output for DGE is from
- Fig. 2: combination of
Fig_pca.R
and14d_GO_Enrich.R
- Fig. 3:
plasticity_analysis.R
- Fig. 4:
11_dapc.R
- Fig. 5:
10b_popoolation_pi.R
- Fig. 6:
15_Phenotype_data_analysis.R
Supplemental:
- Fig. S1:
Fig_S1.R
- Fig. S2:
indiv_gene_fig.md
- Fig. S3:
indiv_gene_fig.md
- Fig. S4:
13_scatter_plot.R
- Fig. S5:
snp_validation.md
- Fig. S6:
13_scatter_plot.R
- Fig. S7:
09_filter_variants.R
- Fig. S8:
venn.R
- Fig. S9:
14d_GO_Enrich.R
- Fig. S10:
14d_GO_Enrich.R