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drpatelhd4straub
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Update docs/usage.md
Co-authored-by: Daniel Straub <[email protected]>
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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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* Use `--featurecounts_feature_type transcript` since the default value `exon` does not contain the required `--featurecounts_group_type gene_biotype` specification.
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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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* `--skip_rseqc` skip RSeQC since features like splice junctions, transcription start (TSS) and ending sites (TES) are less informative in prokaryotes than in eukaryotes.
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* `--skip_biotype_qc` in case biotypes of your RNA data are of no interest.
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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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