Add docs for nf-core#568

drpatelh · Apr 15, 2021 · e9375d5 · e9375d5
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diff --git a/docs/usage.md b/docs/usage.md
@@ -88,6 +88,8 @@ The minimum reference genome requirements are a FASTA and GTF file, all other fi
 * If `--gene_bed` is not provided then it will be generated from the GTF file.
 * If `--additional_fasta` is provided then the features in this file (e.g. ERCC spike-ins) will be automatically concatenated onto both the reference FASTA file as well as the GTF annotation before building the appropriate indices.
 
+When using `--aligner star_rsem`, both the STAR and RSEM indices should be present in the path specified by `--rsem_index` (see [#568](https://github.com/nf-core/rnaseq/issues/568))
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 > **NB:** Compressed reference files are also supported by the pipeline i.e. standard files with the `.gz` extension and indices folders with the `tar.gz` extension.
 
 If you are using [GENCODE](https://www.gencodegenes.org/) reference genome files please specify the `--gencode` parameter because the format of these files is slightly different to ENSEMBL genome files: