Arang Rhie
Hello, no, we have no CADD scores available at the moment. Would be great if someone could contribute and generate this data.
Hello @xiaoguanghuan1, It is likely that the CHM13 allele matched the HG002 allele and went into the assembly on this locus. No hg38 haplotypes were considered during the assembly /...
Hi @duhuipeng , 1. The changing color What you are seeing is the phase block. You can track the switched blocks from `*.phased_block.bed`. Each column in `phased_block.bed` is: ``` ```...
The last column here are the num. kmers found from the haplotype defined as in col. 4. So in your example, 1582 hap2 kmers were found, with no hap1 kmers,...
Merqury is defining a phase block based on how many hap1 or hap2 kmers are found. Once the conditions are met to be decided that a block belongs to hap1,...
What you understood is correct. > Why did this fragment of contig appear in hap1, not in hap2? What you are asking is beyond what Merqury does. It could be...
Hello @dirkjanvw, You could try using [to_hist_for_plotting.sh](https://github.com/marbl/merqury/blob/master/plot/to_hist_for_plotting.sh) for your meryl dbs. For example, ``` sh $MERQURY/plot/to_hist_for_plotting.sh db1.meryl DB1 db2.meryl DB2 > db1_and_db2.hist ``` This generates one histogram file that could...
Hello @HaploTookit , No, there is no direct way to get the NG50 from merqury. I use the `*.phased_block.sizes` to get the NG50 and associated continuity plots. ``` Rscript $MERQURY/plot/plot_block_N.R...
Hi @xiaoaozqd, Could you try something like ``` Rscript plot_spectra_cn.R -f hap.spectra-asm.hist -o hap.spectra-asm -z hap.dist_only.hist -m 250 -n 1000 -t line ``` `-m` and `-n` defines the x_max and...
Hi @goeckeritz , Specify both `-m` and `-n`. I guess you'd need `-m 80` for the x axis. Your default run will leave a message what Y value was used....