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Changed a sentence in README.md
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aljpetri committed Jan 24, 2024
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Expand Up @@ -60,7 +60,7 @@ To only run the isONform algorithm:<br />
isONform_parallel --fastq_folder path/to/input/files --t <nr_cores> --outfolder /path/to/outfolder --split_wrt_batches
```

Note: Please always give absolute paths to the files or folders
Note: Please always use absolute paths to the files or folders

The full isON-pipeline (isONclust, isONcorrect, isONform) can be found [here](https://github.com/aljpetri/isONform/blob/master/isON_pipeline.sh) and is run via:

Expand All @@ -69,6 +69,11 @@ The full isON-pipeline (isONclust, isONcorrect, isONform) can be found [here](ht
```
(Please note that this requires isONclust [LINK](https://github.com/ksahlin/isONclust) and isONcorrect [LINK](https://github.com/ksahlin/isONcorrect) to be installed in addition to isONform)

To receive more information about the arguments used for the isON_pipeline script:
```
./isON_pipeline.sh --help
```

## Outputs <a name="Outputs"></a>
IsONform outputs three main files: transcriptome.fasta, mapping.txt, and support.txt.
For each isoform that isONform reconstructs the id has the following form: x_y_z.
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