Appendix

Appendix: Dependent data

Get dependent data

ChiLin support all species listed on UCSC website, which includes dependent data as we list in species:

• (Must) genome index for your species, we recommended bwa index.
• (Must) chromosome length information text file.
• (Must) standard RefSeq files.
• (Optionally)PhastCons conservation bigwiggle files.
• (Optionally) genome directory containing chromosome separated sequence fasta files
• (Optionally) Union DHS and blacklist regions

We have packaged all dependent data for hg19, hg38, mm9, mm10.

Data details

• First is large disk usage data:

Data Name	Used by	Data Source
genome_index	bwa/bowtie/star	raw fasta indexed files
genome_dir	bwa/bowtie/star	genome fasta files
conservation	conservation_plot.py	wiggle files

Genome version	Raw genome sequence	Masked genome sequence
hg19	hg19_raw	hg19_mask
hg38	hg38_raw	hg38_mask
mm9	mm9_raw	mm9_mask
mm10	mm10_raw	mm10_mask

• Second is small pieces of reference files:

Data Name	Used by	Data Source
chrom_len	samtools	UCSC table browser
dhs	bedtools	Union DHS regions from Cistrome DB
velcro	bedrolls	blacklist regions
geneTable	bedAnnotate	UCSC table browser
contamination	bwa	Mycoplasma genome index(set by --mapper)

• Followings is how we generate these reference files, if you have any species other than hg19/hg38/mm9/mm10, you can find the reference files with the similar ways.

Mycoplasma genome

It seems that Mycoplasma contamination would be a major source of contamination, so we recommended downloading the Mycoplasma fasta for indexing, data is in the link of the mycoplasma genome.

Then index with bwa index -a is mycoplasma.fasta.

BWA Index

download raw genome sequence data, and tar xvfz them and cat *fa > genome.fa. Use the following to index them:

bwa index -a bwtsw genome.fasta

UCSC table browser

Use Browser step by step

• To get refseq files, open UCSC table browser
• Go to the UCSC table browser.
• Select desired species and assembly, such as hg19
• Select group: Genes and Gene Prediction Tracks
• Select track: RefSeq Genes
• Select table: refGene
• Select region: genome
• Select output format: all fields from selected table
• Enter output file: species.refgene
• Hit the 'get output' button
• d*ownload and remove the header line with command,

sed 1d species.refgene > sp.refgene

Conservation score

• (Optional) get Phaston conservation, for most common species version, hg19_conserv, hg38_conserv, mm10_conserv, mm9_conserv and use wigToBigWig to convert them into bigwig, we provide hg19/mm9 conservation score on our server, for other species, just left the chilin.conf conservation section blank. Take hg19 as an example:

wget -r -np -nd --accept=gz http://hgdownload-test.cse.ucsc.edu/goldenPath/hg19/phastCons46way/placentalMammals/
for c in chr*wig*gz
do
bw=${c%phastCons46way.placental.wigFix.gz}bw
echo $bw
gunzip -c $c | wigToBigWig stdin chrom_len $bw  ## chrom_len is where you put your reference chromosome information file
done