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beebdev merged 1 commit into from
Nov 13, 2022
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Update README.md #1

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28 changes: 13 additions & 15 deletions README.md
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Original file line number Diff line number Diff line change
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# RUscripts-R9
This is a fork of the original [RUscript](https://github.com/mattloose/RUscripts) (deprecated system with Python 2 and R7 nanopore data) which we extended to support Python3, R9 nanopore data, and slow5 format.
This is a fork of the original [RUscript](https://github.com/mattloose/RUscripts) (deprecated system that uses Python 2.7 for R7 nanopore data) which we extended to support Python 3.6+, R9.4 nanopore data, and [S/BLOW5 file format](https://www.nature.com/articles/s41587-021-01147-4). Note that we have only extended the *offline RUscripts* component.

## Setting up dependancies to run the updated RUscripts
```sh
cd RUscripts
## Setting up dependancies and RUscripts-R9
```bashsh
git clone https://github.com/beebdev/RUscripts-R9
cd RUscripts-R9
python3 -m venv env
source env/bin/activate
pip3 install --upgrade pip
Expand All @@ -13,22 +14,19 @@ python3 setup.py install

## Running offline RUscripts
To run the software-based updated offline RUscripts on the example Covid-19 dataset:
```sh
cd RUscripts
python3 OfflineReadUntil.py -f dataset/fasta/nCoV-2019.reference.fasta -t MN908947.3:10000-15000 -p 4 -m models/r9.4_450bps.nucleotide.6mer.template.model -w dataset/ncov-testset/slow5 -o RUgOUT -L 3000
```bashsh
python3 OfflineReadUntil.py -f dataset/fasta/nCoV-2019.reference.fasta -t MN908947.3:10000-15000 -p 4 -m models/r9.4_450bps.nucleotide.6mer.template.model -w dataset/ncov-testset/slow5 -o RUgOUT -L 3000 > result.paf
```

## Testing mapping accuracy
With venv activated, install UNCALLED with:
```sh

With the venv activated, install [UNCALLED](https://github.com/skovaka/UNCALLED/tree/uncalled4/uncalled) as:
```bash
pip3 install git+https://github.com/skovaka/UNCALLED.git
```

Generate the paf output by running offline RUscripts and redirecting the stdout output to a file

```sh
python3 OfflineReadUntil.py -f dataset/fasta/nCoV-2019.reference.fasta -t MN908947.3:10000-15000 -p 4 -m models/r9.4_450bps.nucleotide.6mer.template.model -w dataset/ncov-testset/slow5 -o RUgOUT -L 3000 > batch_result.paf
Now compare the generated paf output from offline RUscripts agianst a truthset generated by aligining using Minimap2 (available at dataset/ncov-testset/batch_0.paf) by using [UNCALLED pafstats](https://github.com/skovaka/UNCALLED#pafstats).


python3 OfflineReadUntil.py -f /mnt/d/pr__haru/testset/yeast/GCF_000146045.2_R64_genomic.fna -t NC_001138.5:2000-7000 -p 4 -m models/r9.4_450bps.nucleotide.6mer.template.model -w /mnt/d/pr__haru/testset/yeast/set/ -o RUgOUT -L 3000 > yeast_batch.paf
```
uncalled pafstats -r dataset/ncov-testset/batch_0.paf -n 5000 result.paf
```