Tue Feb  7 12:37:16 PST 2006 - Hiram

The cytobands.bed file here was created with the command:

./runBander.pl ./fishClones.txt ./ISCN800.txt ./setBands.txt /cluster/data/hg18

The runBander script uses the directory /cluster/data/hg18 to
find the chrom sizes.

The fishClones.txt file is made from the fishClones.bed file with
the script:

./createBanderMarkers.pl ./fishClones.bed > ./fishClones.txt

pctSetBands.txt and ISCN800.txt were copied from the hg17 assembly directory:
	/cluster/data/hg17/bed/cytoband/

setBands.txt is created with the script:
./createSetBands.pl ./pctSetBands.txt ./inserts /cluster/data/hg18 100 >
	setBands.txt

And the cytobands.pct.* files are created with the scripts:

./makeBands.pl ./ISCN800.txt /cluster/data/hg18 > ./cytobands.pct.bed
./makeBandRanges.pl ./cytobands.pct.bed > ./cytobands.pct.ranges

The ./inserts file is from: /cluster/data/hg18/inserts

Specifically, the files here are symlinks to their originals:

bander -> /cluster/bin/i386/bander
ISCN800.txt -> /cluster/data/hg18/bed/cytoband/ISCN800.txt
setBands.txt -> /cluster/data/hg18/bed/cytoband/setBands.txt
fishClones.txt -> /cluster/data/hg18/bed/cytoband/fishClones.txt
cytobands.bed -> /cluster/data/hg18/bed/cytoband/cytobands.bed
runBander.pl -> /cluster/bin/scripts/runBander
createBanderMarkers.pl -> /cluster/bin/scripts/createBanderMarkers
cytobands.pct.ranges -> /cluster/data/hg18/bed/cytoband/cytobands.pct.ranges
cytobands.pct.bed -> /cluster/data/hg18/bed/cytoband/cytobands.pct.bed
pctSetBands.txt -> /cluster/data/hg18/bed/cytoband/pctSetBands.txt
fishClones.bed -> /cluster/data/hg18/bed/fishClones/fishClones.bed
inserts -> /cluster/data/hg18/inserts
createSetBands.pl -> /cluster/bin/scripts/createSetBands
makeBands.pl -> /cluster/bin/scripts/makeBands
makeBandRanges.pl -> /cluster/bin/scripts/makeBandRanges