Updated list of other resources used thus far: Google doc
We set out to analyse the set of uniquely expressed, silenced and differentiated genes between the Haploid/Diploid gametophyte and the sporophyte. We performed functional annotation with EnTAP, and further GO enrichment was performed using GOseq.
- Gathered gene IDs from the lists of DE genes and uniquely silenced genes
- Ran EnTAP against Physcomitrium patens and Arabidopsis thaliana
- Used the gene IDs from the output of EnTAP as an input to GOseq.
We developed a list of repeats with coordinates using repeat modeler and then summarized the proportion of each repeat type and created a circos plot of their location across the genome including per chromosome.
- Run RepeatModeler.sh (Funaria_analysis/Repeat_analysis/scripts)
- Trim the GFF file to only 26 scaffolds (/archive/projects/EBP/Funaria_repeats/repeatmodeler/Funaria_Genome_Scaffold_mask/Funaria_26scaffolds.gff)
- Summary of types of repeats:
Proportion and number of unique:
| Element | Number | Total | Proportion |
|---|---|---|---|
| Copia | 67 | 495 | 0.135 |
| Gypsy | 92 | 495 | 0.189 |
| Helitron | 15 | 495 | 0.031 |
| Unknown | 305 | 495 | 0.612 |
- Summary of length of repeats:
| Type | Length | Total | Proportion |
|---|---|---|---|
| DNA/Kolobok-H | 83733 | 113490427.2 | 0.000737798 |
| DNA/Zisupton | 31265 | 113490427.2 | 0.000275486 |
| RC/Helitron | 1694599 | 113490427.2 | 0.014931647 |
| CRNA | 176104 | 113490427.2 | 0.001551708 |
| Simple_repeats | 28120 | 113490427.2 | 0.000247774 |
| SINE? | 52760 | 113490427.2 | 0.000464885 |
| snRNA | 35734 | 113490427.2 | 0.000314864 |
| tRNA | 115561 | 113490427.2 | 0.001018244 |
| unknown | 9530951 | 113490427.2 | 0.08398022 |
| LTR/Copia | 60956975 | 113490427.2 | 0.53711116 |
| LTR/Gypsy | 40784625.2 | 113490427.2 | 9.359366214 |