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update README
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sfchen committed Oct 13, 2021
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Expand Up @@ -175,10 +175,11 @@ gencore -i in.bam -o out.bam -r hg19.fa -s 1
```
gencore -i in.bam -o out.bam -r hg19.fa -s 1 --score_threshold=9
```
If you want to obtain fewer but ultra clean data, you can enable the `duplex_only` option, and increase the `supporting_reads` and the `ratio_threshold`:
If you want to obtain fewer but ultra clean data, and your data has UMI, you can enable the `duplex_only` option, and increase the `supporting_reads` and the `ratio_threshold`:
```
gencore -i in.bam -o out.bam -r hg19.fa --duplex_only -s 3 --ratio_threshold=0.9
```
Please note that only UMI-integrated paired-end data can be used to generate duplex consensuses sequences.

# UMI format
`gencore` supports calling consensus reads with or without UMI. Although UMI is not required, it is strongly recommended. If your FASTQ data has UMI integrated, you can use [fastp](https://github.com/OpenGene/fastp) to shift the UMI to read query names. 
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