@@ -188,7 +188,7 @@ EDTA will produce multiple outputs:
...
@@ -188,7 +188,7 @@ EDTA will produce multiple outputs:
make sure to delete headers starting with ### in the respecrtive files, they can't be read by numpy!
make sure to delete headers starting with ### in the respecrtive files, they can't be read by numpy!
### Fig. 2: EDTA results analysis:
### Fig. 2: EDTA results analysis:
The [code for the results presented in Fig.2](https://git.nfdi4plants.org/hhu-plant-biochemistry/triesch2023_brassicaceae_transposons/-/blob/main/workflows/Fig2_genome_size.ipynb) contains a basic analysis of the `EDTA` results. The genome size were hard-coded from the amount of bases in the respective genome .fasta files. It was distinguished between the "FRAGMENTED" and "INTACT" outputs of `EDTA`.
The [code for the results presented in Fig.2](/blob/main/workflows/Fig2_genome_size.ipynb) contains a basic analysis of the `EDTA` results. The genome size were hard-coded from the amount of bases in the respective genome .fasta files. It was distinguished between the "FRAGMENTED" and "INTACT" outputs of `EDTA`.
### Fig.3: TE classes
### Fig.3: TE classes
The [code for Fig.3](https://git.nfdi4plants.org/hhu-plant-biochemistry/triesch2023_brassicaceae_transposons/-/blob/main/workflows/Fig3_TE_types.ipynb) contains a breakdown of the TE classes as analyzed in `EDTA`. The lengths of the TEs (as numbers of base pairs) were counted and compared.
The [code for Fig.3](https://git.nfdi4plants.org/hhu-plant-biochemistry/triesch2023_brassicaceae_transposons/-/blob/main/workflows/Fig3_TE_types.ipynb) contains a breakdown of the TE classes as analyzed in `EDTA`. The lengths of the TEs (as numbers of base pairs) were counted and compared.
