Odd Spectra.asm plot generated

[ap1438]

Hi,

I ran merquery for assembly evaluation in trio mode and got this weird plot. I cannot understand what's wrong in the assembly.

I ran the same command for other 2 assemblies and the plots were perfect as shown in the example.

[arangrhie]

Hi,
Try re-generating the plots with -m -n options. More in: #27.

[ap1438]

Thankyou for quick reply.

I generated the new plot. But it looks odd.

You can see there are peaks of both the assemblies from 0 -50 in the x axis with high frequency low coverage peaks (As far as my understanding these are sequencing errors). which is again not usual what I have seen in other two assemblies.
Can you please explain what this means. Does it mean contamination or sequencing error, or any other problem is there with the assemblies.

[arangrhie]

It looks like some junk sequence that got into your assembly.
You could try fish out where the low-frequency kmers are present along your two assemblies.
For example,

meryl less-than 25 read-db.meryl output lowcov.meryl
meryl intersect lowcov.meryl asm1.meryl output asm1_lowcov.meryl
# in bed format
meryl-lookup -bed -sequence asm1.fasta -mers asm1_lowcov.meryl | bedtools merge -i - > asm1_lowcov.bed
# in wig format
meryl-lookup -wig-count asm1_lowcov.wig

And apply the same on asm2.
The .wig file will have values of the multiplicity seen in the low_cov.meryl.
See where most of the low-coverage kmers are present. Fish out some contigs with multiple hits, and try a BLAST search or so. It will show up if it was a contaminant.

[ap1438]

Thank you for your suggestion.
I was trying to change the y axis for this plot but it seems that i am not able to change the y axis with -n parameter.

plot_spectra_cn.R -m 250 -n 500000 -f hifi_S33.spectra-asm.hist -o check_hifi_33_asm -z hifi_S33.dist_only.hist
Loading required package: argparse
Loading required package: ggplot2
Loading required package: scales
[1] "x_max: 250"
[1] "y_max: 92475499.6"
[1] "## Line graph"
[1] "## Area under the curve filled"
[1] "## Stacked"
Warning messages:
1: The size argument of element_rect() is deprecated as of ggplot2 3.4.0.
ℹ Please use the linewidth argument instead.
2: Using size aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use linewidth instead.

I get this . Am i doing someting wrong with the command.

[arangrhie]

That is because Merqury tries to show the error (dist_only.hist) results by default.
If you aren't interested in it, try generate one without the -z hifi_S33.dist_only.hist.

Rscript  $MERQURY/plot/plot_spectra_cn.R -m 250 -n 500000 -f hifi_S33.spectra-asm.hist -o check_hifi_33_asm

Best,
Arang