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Co-authored-by: Harshil Patel <[email protected]>

docs/usage.md

@@ -117,7 +117,7 @@ If you would like to reduce the number of reads used in the analysis, for exampl
 ## Alignment options
 
 :::note
-Not currently available using ARM architecture ('-profile arm')
+The `--aligner hisat2` option is not currently supported using ARM architecture ('-profile arm')
 :::
 
 By default, the pipeline uses [STAR](https://github.com/alexdobin/STAR) (i.e. `--aligner star_salmon`) to map the raw FastQ reads to the reference genome, project the alignments onto the transcriptome and to perform the downstream BAM-level quantification with [Salmon](https://salmon.readthedocs.io/en/latest/salmon.html). STAR is fast but requires a lot of memory to run, typically around 38GB for the Human GRCh37 reference genome. Since the [RSEM](https://github.com/deweylab/RSEM) (i.e. `--aligner star_rsem`) workflow in the pipeline also uses STAR you should use the [HISAT2](https://ccb.jhu.edu/software/hisat2/index.shtml) aligner (i.e. `--aligner hisat2`) if you have memory limitations.