diff --git a/README.md b/README.md index 992a5a051..5b2df134b 100644 --- a/README.md +++ b/README.md @@ -166,14 +166,14 @@ The default heuristic for double-ended barcodes is to look for them on either en The output from `dorado basecaller` can be demultiplexed into per-barcode BAMs using `dorado demux`. e.g. ``` -$ dorado demux -o --no-classify +$ dorado demux --output-dir --no-classify ``` This will output a BAM file per barcode in the `output-dir`. The barcode information is reflected in the BAM `RG` header too. Therefore demuxing is also possible through `samtools split`. e.g. ``` $ samtools split -u /unclassified.bam -f "/_%!.bam" -`` +``` However, `samtools split` uses the full `RG` string as the filename suffix, which can result in very long file names. We recommend using `dorado demux` to split barcoded BAMs. #### Classifying existing datasets