Centromere Telomere locations

BRASS needs to know where the centromere and telomere regions start and end.

This data is accessible for many species from UCSC:

(image is an example, select relevant species/build)

Select the relevant species and build, along with the fields indicated above. You will need to set a filters, see following information also.

Unfortunately UCSC change the data in the tables quite regularly. In more recent builds it appears that there is a specific Centromeres track. If the above didn't give centromere outputs you will need to gather data from the new table getting min/max values for each chromosome. ⚠️ The output from UCSC table browser is not sorted and you will need to merge ranges on the same chromosome.

Using the resulting data you construct a tab separated file following the format of this file:

chr	ptel	cen_start	cen_end	qtel	comment
1	750000	121270001	150000000	249220001	.
2	10000	89330001	95390000	242950001	.

If you have no centromeres, set ptel and cen_start to 0, assigning the usable seq range to cen_end and qtel.

If you have no telomere or centromere data at all you can use this to generate the file:

export MITO='Mito'
perl -ane 'printf qq{%s\t0\t0\t1\t%d\t.\n},$F[0],$F[1];' genome.fa.fai | grep -v $MITO > centTelo.tsv