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Add docs mirtop #482

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Nov 12, 2024
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Add docs mirtop #482

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8c64601
update docs
atrigila Nov 12, 2024
b1513c6
update changelog
atrigila Nov 12, 2024
d04cc55
fix changelog
atrigila Nov 12, 2024
181039a
Update docs/usage.md
atrigila Nov 12, 2024
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3 changes: 2 additions & 1 deletion CHANGELOG.md
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Expand Up @@ -5,7 +5,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

## Dev vTBD - TBD - TBD

- [[#477]](https://github.com/nf-core/smrnaseq/issues/481) - Fix [MIRTOP_STATS IndexError](https://github.com/nf-core/smrnaseq/issues/477) - Fix mirtop process execution when mirgenedb is used.
- [[#481]](https://github.com/nf-core/smrnaseq/pull/481) - Fix [MIRTOP_STATS IndexError](https://github.com/nf-core/smrnaseq/issues/477) - Fix mirtop process execution when mirgenedb is used.
- [[#482]](https://github.com/nf-core/smrnaseq/pull/482) - Update documentation regarding MirgeneDB input files.

## v2.4.0 - 2024-10-14 - Navy Iron Boxer

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4 changes: 4 additions & 0 deletions docs/usage.md
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Expand Up @@ -45,6 +45,10 @@ If MirGeneDB should be used instead it needs to be specified using `--mirgenedb`
- `mirgenedb_mature`: This parameter should point to the FASTA file containing mature miRNA sequences. The file can be manually downloaded from [MirGeneDB](https://mirgenedb.org/download).
- `mirgenedb_hairpin`: This parameter should point to the FASTA file containing precursor miRNA sequences. Note that MirGeneDB does not offer a dedicated hairpin file, but the precursor sequences can be downloaded from [MirGeneDB](https://mirgenedb.org/download) and used instead.

See examples in: [the test-datasets repository of nf-core](https://github.com/nf-core/test-datasets/tree/smrnaseq/MirGeneDB).

> [!NOTE] > `mirtop` is hard-coded to use the `pre` sequences, which originate from the hairpin FASTA, rather than the `pri` sequences, which come from the mature FASTA. Users must provide `pre` files from the start to ensure consistency between the FASTA and GFF files, as the coordinates in the GFF file are referenced to `pre` sequences. This also ensures that names in the BAM file will match those in the GFF.

### Genome

- `fasta`: the reference genome FASTA file
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