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jenmuell
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added adaptations for prokaryotic data below the paragraph reference genomes
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docs/usage.md

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@@ -84,7 +84,7 @@ Changes and parameter specifications for prokaryotes:
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* You can use `--featurecounts_feature_type CDS` in combination with `--featurecoutns_group_type product` but than featureCounts will no longer reflect the biotypes of your RNA. It could be helpful to identify the number of hypothetical proteins.
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* If your execution struggle with Salmon as aligner, change `--alginer` to hisat2.
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* You can skip RSeQC with `--skip_rseqc` since it mainly focus on eukaryotic features like splice junctions, transcription start (TSS) and ending sites (TES)
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* If you aren't iterested in the biotypes of your RNA data, you can skip the whole process with `--skip_biotype_qc`
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* If you aren't interested in the biotypes of your RNA data, you can skip the whole process with `--skip_biotype_qc`
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> **NB:** For older versions of the pipeline the names may be different. Check the paramters docs for details.
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