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@@ -66,10 +66,12 @@ The minimum reference genome requirements are a FASTA and GTF file, all other fi
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- If `--gene_bed` is not provided then it will be generated from the GTF file.
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- 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.
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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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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.
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As of v3.7 of the pipeline, if you are using a genome downloaded from AWS iGenomes and using `--aligner star_salmon` (default) the version of STAR to use for the alignment will be auto-detected (see [#808](https://github.com/nf-core/rnaseq/issues/808)).
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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:
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- The `--gtf_group_features_type` parameter will automatically be set to `gene_type` as opposed to `gene_biotype`, respectively.
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