karyotype problem?

[Mauricio Galdos]

Hi,

I'm really new to CIRCOS and I'm trying to understand exactly what the problem is with my files. I've been banging my head against the wall all day and just cannot figure out why CIRCOS is giving me the following message:

  *** CIRCOS ERROR ***

  Entry in 'chromosomes' parameter [0] mentions chromosome [0] which is not

  defined the karyotype file. Make sure that list_record_delim and

  list_field_delim are defined (see etc/housekeeping.conf) in order for the

  'chromosomes' parameter to be parsed correctly.

I am pretty sure it must have something to do with my karyotype file, but I'm not sure what. Maybe the columns are in the wrong order? I'll keep trying to troubleshoot after I post this.

In any case, I'm a attaching a couple of the files I'm working with (the data file is just the first 10 lines, otherwise it could take a while to upload). I haven't changed many parameters of the cfg file yet because first I am just trying to get the program to work.

Thanks,

Mauricio

[Martin Krzywinski]

Your chromosome names are like this

s160_Muller_A_consensus

but in circos.2.conf you refer to a chromosome named 'chrom'. 

chromosomes                 = chrom

Looking at your karyotype file this chromosome isn't defined anywhere.

Also chromosomes_breaks expects chromosome interval definitions. Here, "no" doesn't make sense and will cause a parse error. If you don't want to crop any ideograms, remove this parameter.

You don't need this parameter is you want to show all the chromosomes in the order that they appear in the karyotype file. 

karyotype = ./dvirkaryotype2.txt

chromosomes_units = 10000

chromosomes_display_default = yes

I'm also seeing

<<include ./housekeeping.conf>>

in your config. This file should be included from the Circos distribution

<<include etc/housekeeping.conf>>

and parameter overridden using the * suffix syntax

<<include etc/housekeeping.conf>>

param* = new_value

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

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[Mauricio Galdos]

Hi Martin,

Thanks for your quick reply. The suggestions you gave me did the trick.

Now I'm running into a very weird issue though.

I am using the exact same files and I have been changing the chromosome name in the conf file to match whichever chromosome I want displayed. However, I can only get the chromosome on the first row to show (In this case, "s160_Muller_A_consensus"). If I change it to "s160_Muller_B_consensus", what I get as an output is a histogram of the Muller_A.

I double-checked my data by plotting it in R so I am sure it must have something to do with the way I am configuring the file.

I am attaching the conf file again in case you want to take a look at it.

Thanks a lot for the help, I really appreciate it.

Mauricio

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[Martin Krzywinski]

If you want to show one chromosome at a time, set

chromosomes_display_default = no

chromosomes = s160_Muller_A_consensus

To show B

chromosomes_display_default = no

chromosomes = s160_Muller_B_consensus

Are you saying that trying this does not work? If so, please email me all the conf/data files and I will test.

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

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