Comments (4)
The plots generated should have a similar naming to this:
nontrio_both.hap1.spectra-cn.fl.png
nontrio_both.hap1.spectra-cn.ln.png
nontrio_both.hap1.spectra-cn.st.png
nontrio_both.hap2.spectra-cn.fl.png
nontrio_both.hap2.spectra-cn.ln.png
nontrio_both.hap2.spectra-cn.st.png
nontrio_both.spectra-asm.fl.png
nontrio_both.spectra-asm.ln.png
nontrio_both.spectra-asm.st.png
nontrio_both.spectra-cn.fl.png
nontrio_both.spectra-cn.ln.png
nontrio_both.spectra-cn.st.png
Plotting type
- fl: un-stacked filled plot
- ln: lun-stacked ine plot
- st: stacked filled plot
What to plot
- spectra-cn: copy number spectrum; show portion of kmers present in 1~4 or more copies in the given fasta
- spectra-asm: assembly spectrum; show portion of kmers exclusively belonging to each fasta, or shared by both
And the same plots are generated for each fasta files (hap1 or hap2).
Plots without hap1 or hap2 are drawn for both fasta files.
I don't see much 'weirdness' around. Seems like the Hi-C version is in a 'diploid' assembly form? It has certainly less missing kmers (read-only, black area) in hap1 compared to the pseudo-haplotype version.
from merqury.
Yes, correct! Also the Hi-C version is for a diploid assembly.
Thanks for the valuable info, and for the interpretation of Merqury's output. What I meant when I mention about the other three plots for each haplotype was exactly this:
nontrio_both.spectra-cn.fl.png
nontrio_both.spectra-cn.ln.png
nontrio_both.spectra-cn.st.png
Now it's all clear. Thanks again!
Matteo
from merqury.
Hi Matteo,
If HiFi reads are the only source of WGS you have, yes, create a db.meryl from this and use it as the reads.meryl.
Ideally, it is recommended to use Illumina WGS, as HiFi reads have biases in certain sequence patterns, thus will favor HiFi assemblies.
You could run Merqury twice;
- on the partially-phased haplotype assemblies
- on the fully phased assembly
however I wouldn't expect much difference because no parental data are available to confirm the phasing state.
Scaffolding with Hi-C wouldn't affect the kmer spectrum unless sequence level modification was performed, such as gap filling or polishing.
How have you run Merqury?
How does the plots look like?
from merqury.
Thanks a lot for the fast answer!
Do you know I had exactly the same thoughts; in fact, I was discussing about that with one of my colleagues to explain him that what I'm getting is most likely the outcome of lacking parental data (Trio binning).
I did run Merqury with partially-phased haplotypes (1), following the output plots:
And with fully-phased haplotypes (2) โ sorry for my bad memory, following the output plots:
I did get also the line plots for both the spectra-cn and spectra-asm (for both hap1 and hap2). However, I also get six additional plots (three for hap1 and three for hap2) that I cannot really understand what they are telling. For now I show you these two figures, I can then attach the other six graphs (just to keep things a bit cleaner).
P.S. column 1 = hap1, column 2 = hap2 and column 3 = assembly spectra
from merqury.
Related Issues (20)
- I don't understand how to get the right K mer size HOT 2
- Is there a script to rerun the plot? HOT 4
- How to deal with Hifi, Ont UL, and hic data together? HOT 7
- The QV value about T2T will be lower HOT 5
- improve phase block HOT 1
- Qustion about Spectra copy number analysis HOT 1
- Completeness, Switch Error๏ผ HOT 1
- Error in f(...) : Graphics API version mismatch HOT 2
- Help with interpreting spectra-cn and spectra-asm plots with Illumina WGS reads HOT 3
- order of mat and pat HOT 1
- error with finding bedtools and argparse HOT 1
- "no module file for 'bedtools', no package 'argparse'" HOT 1
- meryl-lookup failed (# Per seq QV statistics for haplotype 2) HOT 2
- Options to resize? HOT 2
- wildcard is intertpreted as an assembly and not a meryl database
- No plot because ggplot2 deprecation command HOT 4
- Completeness in previous version not appearing/Conda installation compatibility issues HOT 1
- Question about relative position of peaks in trio hapmers plot HOT 2
- Problems encountered when running Merqury with HiFi reads only HOT 4
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from merqury.