Starting with a BED file

Note

These tutorials are still under active development.

Get the sequences in FASTA format from a BED file

For example, you have a BED file for all the exons from hg38. Now you want to get their sequences in FASTA format with care of the orientation of the strands.

from genomkit import GRegions

exons = GRegions(name="exons", load="hg38_exons.bed")
exon_seqs = exons.get_GSequences(FASTA_file=FASTA_hg38)
exon_seqs.write_FASTA(filename="hg38_exons.fasta")

Get TSSs (Transcription Start Sites) and TTSs (Transcription Termination Sites) of genes in a BED file

Given a BED file with gene bodies (Please refer to this tutorial), you can get the TSSs or TTSs regions with the size of 100 bp by the following codes:

from genomkit import GRegions

genes = GRegions(name="genes", load="hg38_genes.bed")
TSSs = genes.resize(extend_upstream=50, extend_downstream=50,
                    center="5prime", inplace=False)
TTSs = genes.resize(extend_upstream=50, extend_downstream=50,
                    center="3prime", inplace=False)
TSSs.write(filename="hg38_TSSs.bed")
TTSs.write(filename="hg38_TTSs.bed")

Merging the nearby peaks in a BED file

Sometimes the peaks in a BED file are cluster together and you want to combine them if their distance is less than a certain value. For example, you want to combine all the peaks if their distance are below 50 bp.

from genomkit import GRegions

peaks = GRegions(name="peaks", load="peaks.bed")
clustered_peaks = peaks.cluster(max_distance=50)
clustered_peaks.write(filename="clustered_peaks.bed")

Sampling the regions randomly in a BED file

You can also randomly sample 1000 regions by the codes below:

from genomkit import GRegions

peaks = GRegions(name="peaks", load="peaks.bed")
samples = peaks.sampling(size=1000, seed=42)
samples.write(filename="peaks_1000_samples.bed")

Find the peaks in one BED file close to the regions in another BED file

Often you want to find the interaction between two BED files, but not simply by overlapping. For example, now you have hg38_promoters.bed and TFBSs.bed and you want to find the TFBSs which are close to the promoters within 1000 bp.

from genomkit import GRegions

promoters = GRegions(name="promoters", load="hg38_promoters.bed")
promoters.extend(upstream=1000, downstream=1000, inplace=True)
TFBSs = GRegions(name="TFBSs", load="TFBSs.bed")
close_TFBSs = TFBSs.intersect(target=promoters, mode="ORIGINAL")
close_TFBSs.write(filename="TFBSs_close_to_promoters.bed")

Generate a heapmap from two BED files: one BED file is used as windows and the other used as the signal

Sometimes your signals (scores) are stored in a BED file (column 5), instead of BEDGraph or BigWig. And now you want to visualize the interactions between these two BED files. For example, DMSs.bed contains the differential methylated CpGs with the score for hypermethylation or hypomethylation. And TSSs.bed include all transcription start sites with a window of 2000 bp. Now you want to visualize their interaction with a heatmap.

Starting with many BED files

When you have multiple BED files and want to investigate the interactions among those sets of genomic elements, you need to use GRegionsSet class. Below are some usage cases.

Test the relevance of multiple peaks in BED files to different biotypes in GTF

For example, you have 4 BED files for different peaks:

peaks_A.bed
peaks_B.bed
peaks_C.bed
peaks_D.bed

And you have generated some BED files for different biotypes in human (Please refer to this tutorial).

hg38_protein_coding_genes.bed
hg38_lncRNA_genes.bed
hg38_snRNA_genes.bed
hg38_miRNA_genes.bed

Now you want to check the overlaps of the peaks with the genes.

from genomkit import GRegionsSet
# load peaks
peaks_dict = {"A": "./peaks_A.bed",
              "B": "./peaks_B.bed",
              "C": "./peaks_C.bed",
              "D": "./peaks_D.bed",}
peaks = GRegionsSet(name="peaks", load_dict=peaks_dict)
# load biotypes
biotypes_dict = {"protein_coding": "./hg38_protein_coding_genes.bed",
                 "lncRNA": "./hg38_lncRNA_genes.bed",
                 "snRNA": "./hg38_snRNA_genes.bed",
                 "miRNA": "./hg38_miRNA_genes.bed",}
biotypes = GRegionsSet(name="biotypes", load_dict=biotypes_dict)
# Get a dataframe for overlapping counts
overlaps = peaks.count_overlaps(query_set=biotypes)
# Visualization

# Testing the association
peaks.test_