dedup determinisitc - use a seed?

[RichardCorbett]

Hi there,

When I run this command multiple times:
{code}
umi_tools dedup -I myBam.bam --extract-umi-method=tag --umi-tag=RX --read-length -S myBam.umi_tools.bam
{code}

I get the same number of reads returned each time, but the exact reads returned each time are different. Is there a way to get the same reads with each run?

thanks
RIchard

[IanSudbery]

To use a seed with umi-tools, use the --random-seed= option.

You might also find you need to set the PYTHONHASHSEED= environment variable as well to make sure hashes are returned in the same order, although I think the sorts should take care of that these days....

This is how we run our tests:

#!/use/bin/env bash
export PYTHONHASHSEED=0
umi_tools dedup --random-seed=123456789 .......

[RichardCorbett]

Perfect. Thanks. Sorry I somehow missed this myself.

[IanSudbery]

I'm closing this. Please reopen if you need more advice.