Input files

Reference gene intervals file

The gene intervals file contains the reference transcription start sites (TSSs) for all genes as BED interval data.

There are two built-in gene interval BED files (human hg38 and mouse mm10 genomes) which have been generated from the refGene data downloaded from the UCSC table browser on 12th July 2019. These can be used when running PEGS by specifying the genome build names on the command line.

For other genome builds and organisms, a custom gene interval file must be generated from refSeq data using the mk_pegs_intervals utility described in Making gene interval files.

Peak set files

Peak-set files are BED files containing ChIP-seq peaks or any other genomic interval data of interest.

The files need to contain three columns with chromosome, start and end positions, for example:

chr1        39756959        39757488
chr1        40278922        40279363
chr1        49032761        49033125
...

The names of the files are used as identifiers in the ouput XLSX and heatmap plot files.

Gene cluster files

The gene cluster files are text files with lists of gene names (one gene per line) which make up the cluster, for example:

Ahctf1
Aif1l
Amd1
Asnsd1
...

The names of the files are used as the identifiers for the clusters in the ouput XLSX and heatmap plot files.

TADs file

The TADs (Topologically Associating Domains) file is a BED file containing intervals which defines a set of TAD boundaries to be used in a supplementary enrichment analysis. This analysis uses the TAD intervals instead of the genomic distances.

The files need to contain four columns with chromosome, start and end positions, and a name, for example:

chr1        3009919 4369919 TAD1
chr1        4369919 4769919 TAD2
chr1        4769919 6209919 TAD3
...