circos error - no change to housekeeping.conf

Question

[Obex33]

Hi,

I want to plot a histogram of my mapped reads to Virus genome. I keep getting the error "but the maximum is currently set at [25000]. To increase this number change max_points_per_track in etc/housekeeping.conf." even though I had set my max to 50000"

I checked the max with circos -cdump :max but the maximum would not change from 25000. How can I fix this error and plot mapped reads per base?

Thank you for your help

####This is my circos.conf file####

karyotype = EBV_Karyotypes.txt
chromosomes_units = 100000

<<include etc/colors_fonts_patterns.conf>>
<<include etc/housekeeping.conf>>

# IMAGE
<image>
<<include image.conf>>
</image>

# IDEOGRAM
<ideogram>
<spacing>
default = 1u
break = 1u
</spacing>
radius           = 0.9r
thickness        = 100p
fill             = yes
stroke_color     = black
stroke_thickness = 10p
show_label       = yes
label_radius     = 1.05r
label_size       = 80p
label_parallel   = yes
</ideogram>

# PLOTS
<plots>
type       = histogram
color      = black
fill_under = yes
thickness  = 1
<plot>
file = test.txt
r0   = 0.75r
r1   = 0.98r
min  = 0
max  = 50000
<rules>
<rule>
condition = 1
fill_color = eval(sprintf("rdbu-7-div-%d",remap_int(var(value),0,18000,1,7)))
</rule>
</rules>
</plot>

</plots>

Answer 1

[mbk0asis]

I'm not sure if this can help you, but I found following sentence in the circos best practice page.

"If your data is sampled more finely than this, you will not see any structure in it because multiple data points will be assigned to the same pixel. In general, if you have more than 10,000 data points in any track, consider downsampling. "

Why don't you try downsampling by merging bins or something?

Answer 2

[tothepoint]

Valid point by @mbk0asis. Why not reduce the size by either increasing binsize or use some filter in your data otherwise there will be noise all over the chromosome. Although you can get the output by looking into etc folder (most probably) and just change the parameter in housekeeping.conf file

max_points_per_track = 50000