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Add note about running the tool on multiple files
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CedricHermansBIT committed Feb 21, 2024
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Expand Up @@ -28,6 +28,8 @@ htseq-count-rust alignments.bam genes.gtf
htseq-count-rust -s no -t exon -i gene_id -m intersection-strict -d , -a 10 -n 8 --nonunique all --secondary-alignments ignore --supplementary-alignments ignore -o alignments_out.sam alignments.bam genes.gtf
```

Note: currently, only one SAM/BAM file can be provided. If you want to run the tool on multiple files, you will need to run them separately.

### Options

The following options are currently supported:
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