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Download raw data and set up home folder

All of the following steps are in pipeline_setup.sh.

Please read through each step and customize, before running

bash pipeline_setup.sh

Designate the cell line and HiC resolution that you want to run PhiMRF on.

Example:

cellline=GM12878
resolution=10kb

Designate home directory

Example:

homedir=/home/nzhou/hic/rao2014/GM12878_10kb/

Make folders for RNA-seq data

mkdir $homedir/rnaseq
mkdir $homedir/rnaseq/gene_names

Make folders for intra-chromosomal and inter-chromosomal

for int in 'intra', 'inter'
do
	mkdir $homedir/$int
	mkdir $homedir/$int/raw
	mkdir $homedir/$int/norm
	mkdir $homedir/$int/data
	mkdir $homedir/$int/data/y
	mkdir $homedir/$int/info
	mkdir $homedir/$int/genepairs
done
mkdir $homedir/intra/linear

Download intra-chromosomal HiC data (large file)

wget ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE63nnn/GSE63525/suppl/GSE63525_"$cellline"_combined_intrachromosomal_contact_matrices.tar.gz -P $homedir/intra/raw

You can also download manually from their GEO repository. Make sure to save the downloaded file in $homedir/intra/raw

Extract intra-chromosomal HiC data (could take a while)

Only unzip the desired resolution, normalization method and filter.

Example:

filter=MAPQGE30
norm=KR

See Supplemental 1 (Extended Experimental Procedure) of Rao et al 2014 (PMID: 25497547) for details.

tar -xvzf $homedir/intra/raw/GSE63525_"$cellline"_combined_intrachromosomal_contact_matrices.tar.gz -C $homedir/intra/raw/ --strip-components 4 --wildcards GM12878_combined/"$resolution"_resolution_intrachromosomal/chr*/"$filter"/*.{RAWobserved,"$norm"norm}

Download inter-chromosomal HiC data (large file)

wget ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE63nnn/GSE63525/suppl/GSE63525_"$cellline"_combined_interchromosomal_contact_matrices.tar.gz -P $homedir/inter/raw

You can also download manually from their GEO repository. Make sure to save the downloaded file in $homedir/inter/raw

Extract inter-chromosomal HiC data (could take a while)

tar -xvzf $homedir/inter/raw/GSE63525_"$cellline"_combined_interchromosomal_contact_matrices.tar.gz -C $homedir/inter/raw/ --strip-components 4 --wildcards GM12878_combined_interchromosomal/"$resolution"_resolution_interchromosomal/chr*_chr*/"$filter"/*.{RAWobserved,"$norm"norm}

(Optional!) Download Ensembl gene ID and coordinates

Default Ensembl release: 90

This step is optional, only carry out this step if you are want to use another Ensembl release.

To download another release,

  1. Go to biomart.
  2. Select "Attributes" on the lefthand column, in the expanded table of "GENE", select "Gene stable ID", "Chromosome/scaffold name", "Gene start (bp)" and "Gene end (bp)"; in the expanded table of "External References", select "NCBI gene ID".
  3. Save the downloaded file as ../1rnaseq_processing/ensembl_map_coding.txt

Download RNA-seq data

The RNA-seq quantification data are downloaded from ENCODE. Make sure the cell line of your RNA-seq file agrees with the cell line of your HiC data.

If you wish to use non-ENCODE RNA-seq quantification file, make sure the file follows RSEM's output format.

Note: The first column should be "gene_id" and second column should be "transcript_id", contrary to the above document.

The quantification metric used in this project is the 8th column: "posterior_mean_count"

Example for GM12878 (two isogenic replicates):

wget https://www.encodeproject.org/files/ENCFF781YWT/@@download/ENCFF781YWT.tsv -P $homedir/rnaseq/
wget https://www.encodeproject.org/files/ENCFF680ZFZ/@@download/ENCFF680ZFZ.tsv -P $homedir/rnaseq/

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