Cytoband

BRASS needs cytoband file to run pcf function in copynumber package. This data is accessible for many species from UCSC: Select the relevant species and build, along with the fields indicated below.

Warning: please make sure that the chromosome nomenclature is identical to the header in bam file else edit the file to match with bam header.

Provide resulting file to -cytoband option in brass.

Example file format:

#chrom  chromStart      chromEnd        name    gieStain
chr1    0       2300000 p36.33  gneg
chr1    2300000 5400000 p36.32  gpos25
chr1    5400000 7200000 p36.31  gneg
chr1    7200000 9200000 p36.23  gpos25
chr1    9200000 12700000        p36.22  gneg

If no cytoband information is available:

echo '#chrom  chromStart      chromEnd        name    gieStain' \
&& cut -f 1,2 genome.fa.fai \
| perl -ane 'print join(qq{\t}, $F[0],0,$F[1],$F[0],q{gneg}).qq{\n};' > cytoband.txt

Please note you should ensure only the main contigs are included, as per the centTelo.txt file.