Arang Rhie

Hello, you could use this script in Merqury: https://github.com/marbl/merqury/blob/master/eval/false_duplications.sh This looks into the 1st and 2nd peak of the spectra-cn plot, and counts what is seen more than once assuming...

Hello Mojtaba @m-jahani , Apologies for the delayed reply! This totally slipped through. Thanks for reading the paper in detail!! That sentence was left in error as a mistake (Ouch!!)....

@aafshinfard how big is the total file size?

Hello @zmz1988 , Thanks, weird that no plots are generated! Have you checked the log? What does the spectra-cn.log say? Feel free to post the log here. Best, Arang

Hi @zmz1988 , it seems like the required input files aren't completely present from your run. Do you see anything else in the log, above the R log?

Hi @zmz1988 again, So the R script needs 2 files: C_necat_merge.merged_C_necat_ONTR_PBasm_large.spectra-cn.hist C_necat_merge.merged_C_necat_ONTR_PBasm_large.only.hist I suspect one (or both?) *.hist file above is empty. Also, merged_C_necat_ONTR_PBasm_large.0.meryl using 0 memory is also suspicious......

Hi @Simon-Huang1 , although it is know that Illumina reads do have GC biases, the HiFi reads are still a bit error prone in homopolymers, which affects a larger amount...

Hi @ASLeonard , I assume the illum_only also comes from a filtered version? It is not possible to entirely remove biases; I'd say provide QVs measured from each platforms and...

Hello, 1. The conda version was a voluntary contribution from @EdHarry. My knowledge to conda is very limited. If you have a simple solution for this, suggestions are welcome. 2....

The pat.meryl and mat.meryl are the pat.hapmer.meryl and mat.hapmer.meryl, generated with `hapmers.sh`.