Formatting data files for JBrowse

Chromosome IDs

All features in data files need to use these chromosome IDs:

• I
• II
• III
• chr_II_telomeric_gap
• mitochondrial
• mating_type_region

Data directories

On oliver1:

• main directory: /data/pombase/external_datasets/
• original files, one sub-directory per dataset: /data/pombase/external_datasets/originals
• processed files, with correct chromosome IDs, sorted and indexed: /data/pombase/external_datasets/processed/

The processed directory is rsynced to:

• /home/ftp/pombase/external_datasets/ on the Babraham server

BED / TabixBED

sort -k1,1 -k2,2n -k3,3n BranchPoint_v2.bed > BranchPoint_v2.sorted.bed
bgzip BranchPoint_v2.sorted.bed
tabix -p bed BranchPoint_v2.sorted.bed.gz

WIG

for i in `find . -name '*.wig'`
do
  BW=${i%.wig}.bw
  echo $i
  wigToBigWig $i ~/pombe/chromosome.sizes $BW
done

Where chromosome.sizes is:

chr_II_telomeric_gap    20000
mitochondrial   19431
mating_type_region      20128
III     2452883
II      4539804
I       5579133

SAM/BAM

JBrowse needed sorted, indexed BAM files. Both the .bam and .bam.bai need to be on the server