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Processing data

BigWig files

In the clodius repository:

wget http://hgdownload.cse.ucsc.edu/goldenpath/hg19/encodeDCC/wgEncodeCaltechRnaSeq/wgEncodeCaltechRnaSeqHuvecR1x75dTh1014IlnaPlusSignalRep2.bigWig
python scripts/tile_bigWig.py ~/Downloads/wgEncodeCaltechRnaSeqHuvecR1x75dTh1014IlnaPlusSignalRep2.bigWig --output-file ~/Downloads/wgEncodeCaltechRnaSeqHuvecR1x75dTh1014IlnaPlusSignalRep2.hitile

Cooler files

wget ftp://cooler.csail.mit.edu/coolers/hg19/Rao2014-GM12878-DpnII-allreps-filtered.1000kb.cool
python scripts/recursive_agg_onefile.py Rao2014-GM12878-DpnII-allreps-filtered.1000kb.cool

Gene annotation files

wget https://s3.amazonaws.com/pkerp/public/geneAnnotationsExonUnions.bed
python scripts/tileBedFileByImportance.py test/sample_data/geneAnnotationsExonsUnions.short.bed --max-per-tile 60 --importance-column 5 test/sample_data/gene_annotations.short.db