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readme fixes
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hasindu2008 committed Feb 11, 2019
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6 changes: 2 additions & 4 deletions README.md
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Expand Up @@ -56,8 +56,6 @@ If your CUDA library is not in the default location /usr/local/cuda/lib64, point
```
make cuda=1 CUDA_LIB=/path/to/cuda/library/
```
For instance, it can be something like `/usr/local/cuda-8.0/lib64`. If your system is 32 bit it should be `lib` instead of `lib64`.

Visit [here](https://hasindu2008.github.io/f5c/docs/cuda-troubleshoot) for troubleshooting CUDA related problems.

## Usage
Expand All @@ -71,7 +69,7 @@ Visit the [man page](https://hasindu2008.github.io/f5c/docs/commands) for all th

### Example

Follow the same steps as in [Nanopolish tutorial](https://nanopolish.readthedocs.io/en/latest/quickstart_call_methylation.html) while replacing `nanopolish` with `f5c`. If you only want to perform a quick test of f5c without aligning reads :
Follow the same steps as in [Nanopolish tutorial](https://nanopolish.readthedocs.io/en/latest/quickstart_call_methylation.html) while replacing `nanopolish` with `f5c`. If you only want to perform a quick test of f5c :
```sh
#download and extract the dataset including sorted alignments
wget -O f5c_na12878_test.tgz "http://genome.cse.unsw.edu.au/tmp/f5c_na12878_test.tgz"
Expand All @@ -83,6 +81,6 @@ f5c call-methylation -b chr22_meth_example/reads.sorted.bam -g chr22_meth_exampl
```

## Acknowledgement
This extensively reuses code and methods from [Nanopolish](https://github.com/jts/nanopolish).
This reuses code and methods from [Nanopolish](https://github.com/jts/nanopolish).
The event detection code is from Oxford Nanopore's [Scrappie basecaller](https://github.com/nanoporetech/scrappie).
Some code snippets have been taken from [Minimap2](https://github.com/lh3/minimap2) and [Samtools](http://samtools.sourceforge.net/).
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