Getting a bed file of kmers in assembly but not in reads

mwykes commented 3 years ago

Firstly, thanks for this very useful tool!

I'd like to create a bed file annotating kmers in my assembly which are not in the reads.

As far as I can see, this is done as part of spectra-cn.sh by running

meryl-lookup -bed -sequence $asm_fa -mers ${asm}.0.meryl > ${asm}_only.bed

However, when I try running this, meryl-lookup gives me an error message:

Unknown option '-bed'.
No report-type (-existence, etc) supplied.

I'm using meryl-lookup v1.2 within the merqury conda package.

Does meryl-lookup no longer support bed output, or am I missing something? Is there another way to do this?

Thanks, Mike

arangrhie commented 3 years ago

Hi Mike,

Use the latest meryl from https://github.com/marbl/meryl, or use the merqury script in your conda package.

Thanks, Arang

mwykes commented 3 years ago

Thanks @arangrhie.

In the version of spectra-cn.sh in my conda environment, I found an alternative command that did work

meryl-lookup -dump -memory 6 -sequence $asm_fa -mers ${asm}.0.meryl | awk '$(NF-4)=="T" {print $1"\t"$(NF-5)"\t"($(NF-5)+21)}' > ${asm}_only.bed

Apologies for not checking this before.

Mike

marbl / merqury