Sometimes we want to have sets of SNPs readily accessible for analysis. We may place such sets in the named subfolders under the [dir]/custom_data/fois/[organism]/ folder. The names of the subfolders will serve as the descriptions of the sets of SNPs, e.g., *gwasCatalog".
An example of the fois folder may look like:
/home/testuser/Documents/db_1.01_05.12.2014/custom_data/fois/hg19/GWAStest1/*.bed
/home/testuser/Documents/db_1.01_05.12.2014/custom_data/fois/hg19/GWASrand/*.bed
/home/testuser/Documents/db_1.01_05.12.2014/custom_data/fois/hg19/SNPsCommonRand/*.bed
/home/testuser/Documents/db_1.01_05.12.2014/custom_data/fois/hg19/GWAScatalogFull/*.bed
Some regulatory datasets contain information about different biologically relevant features combined together. An example of such combined regulatory datasets is wgEncodeRegTfbsClusteredV3, containing experimentally detected transcription factor binding sites from 161 different transcription factors. We may want to consider the data for each transcription factor separately. We process such combined data using the extract_UCSC.py script (see the db subfolder in the source code). We place extracted BED files in the [dir]/custom_data/gfs/hg19/tfbsEncode folder. The tfbsEncode GFs will be accessible through GenomeRunner's web interface.
It is a good idea to remove special characters from file names, if any, by running:
for FILE in *.bed; do mv -v "$FILE" $(echo "$FILE" | tr ' ' '_' | tr -d '[{}(),!]' | tr -d "'" | tr -d '`' | tr '[A-Z]' '[a-z]' | sed 's/_-_/_/g'); done
An example of the gfs folder may look like:
/home/testuser/Documents/db_1.01_05.12.2014/custom_data/gfs/hg19/tfbsEncode/*.bed
/home/testuser/Documents/db_1.01_05.12.2014/custom_data/gfs/hg19/H3K4me3/*.bed
/home/testuser/Documents/db_1.01_05.12.2014/custom_data/gfs/hg19/gwasCatalog/*.bed
/home/testuser/Documents/db_1.01_05.12.2014/custom_data/gfs/hg19/chromStates/*.bed
Random SNP sets are used to check for lack of enrichment. They can be generated from a background file using the following command:
for i in {10..19}; do n=$((2**i)); zcat snp128.bed.gz | shuf | head -n $n > rndsnp128_$n.bed; done
The logic here is to generate random SNP sets of different sizes. The sizes are determined by the power of 2 from {10..19} range, so the first set will contain 2^10=1024 random SNPs, the second - 2^11 etc.
This folder contains organism-specific .BED file (BED6) for conversion of the lists of rsIDs into genomic coordinates. For example, for Homo Sapiens this folder may look like:
rsid_conversion/hg19/snp138.bed
The genomic coordinates and rsIDs from the snp138.bed file are used to cross-map user-provided lists of rsIDs with genomic coordinates.