Wrong centormere coordinates

[ivan-balashov]

Hi! thanks for your great package!
Looks like there is an issue with centromere coordinates for some chromosomes in CNAqc::chr_coordinates_GRCh38

because if I get them from USCS I've got this

You can got same with this command

curl -s "http://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/cytoBand.txt.gz" | gunzip -c | grep acen | sort -V -k1,2 | awk 'BEGIN {print "chromosome\tstart\tend"} {print $1 "\t" $2 "\t" $3}' > centromere.txt

My issue not about exact bases only but there are same start and end of centromere(e.g. chr2 and chr4) which is not good;
Thanks!

[caravagn]

Hi, thanks will look into this asap.

[AliceAntonello]

Hi @ivan-balashov , thank you for raising this issue. The centromere coordinates reported in CNAqc::chr_coordinates_GRCh38 are taken from http://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/centromeres.txt.gz, they differ from the ones you are referring to in the ways they were generated, you can find more details here https://genome.ucsc.edu/cgi-bin/hgTables?db=hg38&hgta_group=map&hgta_track=centromeres&hgta_table=centromeres&hgta_doSchema=describe+table+schema.
We suggest you to directly modify the object if you need another set of coordinates.

[caravagn]

Hi @AliceAntonello

Your proposal is not consistent with the current design of CNAqc because it is not possible for a user to modify the centromere coordinates obtained by get_reference

https://github.com/caravagnalab/CNAqc/blob/master/R/get_reference.R

Please think of a way in which this becomes possible (we can add this as a feature). I am changing the issue to enhancment.

[caravagn]

This might be handled together with adding support for mouse coordinates @vvvirgy. Can you handle it?

You need to

• add an RDA for the mouse reference as for others
• update the reference getter

[caravagn]

Ping @vvvirgy

[caravagn]

Last time I ping this @vvvirgy