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Download test data
The two replicates are isogenic replicates (biological). A more detailed explanation of the various types of replicates can be found here.
Links to the replicate bam files provided below.
wget https://www.encodeproject.org/files/ENCFF198CVB/@@download/ENCFF198CVB.bam -O rep1.bam
wget https://www.encodeproject.org/files/ENCFF488CXC/@@download/ENCFF488CXC.bam -O rep2.bam
Now download the control for the experiment, which is available here:
Link provided below
wget https://www.encodeproject.org/files/ENCFF023NGN/@@download/ENCFF023NGN.bam -O control.bam
Finally, download the reference files. In the example below, some preprocessing is required to filter out unwanted chromosomes from the hg38.chrom.sizes file. Additionally, the blacklist file shown is specific to hg38, and should be replaced with a genome-specific blacklist if alternative genomes are used.
Available Blacklists:
For those interested in using the blacklists, a current version for dm3, dm6, ce10, ce11, mm10, hg19, and hg38 are available in the lists/ folder at https://github.com/Boyle-Lab/Blacklist/
Please cite:
Amemiya, H.M., Kundaje, A. & Boyle, A.P. The ENCODE Blacklist: Identification of Problematic Regions of the Genome. Sci Rep 9, 9354 (2019). https://doi.org/10.1038/s41598-019-45839-z
# download genome refrence
wget https://www.encodeproject.org/files/GRCh38_no_alt_analysis_set_GCA_000001405.15/@@download/GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta.gz \
-O hg38.genome.fa.gz | gunzip
# index genome reference
samtools faidx hg38.genome.fa
# download chrom sizes
wget https://www.encodeproject.org/files/GRCh38_EBV.chrom.sizes/@@download/GRCh38_EBV.chrom.sizes.tsv
# exclude alt contigs and chrEBV
grep -v -e '_' -e 'chrEBV' GRCh38_EBV.chrom.sizes.tsv > hg38.chrom.sizes
rm GRCh38_EBV.chrom.sizes.tsv
# make file with chromosomes only
awk '{print $1}' hg38.chrom.sizes > chroms.txt
# download blacklist
wget https://www.encodeproject.org/files/ENCFF356LFX/@@download/ENCFF356LFX.bed.gz -O blacklist.bed.gz
gunzip blacklist.bed.gz