How to use bedtools to predict target genes in chip_seq data

This article introduces the relevant knowledge of "how to use bedtools to predict the target gene of chip_seq data". In the operation process of actual cases, many people will encounter such difficulties. Next, let Xiaobian lead you to learn how to deal with these situations! I hope you can read carefully and learn something!

Usually, when analyzing target genes corresponding to peak regions, a certain length of regions upstream and downstream of transcription start site TSS will be selected as candidate target gene ranges. This article introduces how to use bedtools to analyze overlap between peak and TSS regions, so as to obtain target genes. It can be divided into the following steps:

1. Get the TSS locus information corresponding to the species

Take hg38 as an example, you can get the refFlat file corresponding to the species through the FTP service of UCSC, the link is as follows

http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/

refFLat and refGene have the same information recorded in these two files, refFlat file has fewer columns, here we choose to download refFlat.txt.gz, the contents of this file are as follows

In the original file, there is no title in the first row. I manually added the title to describe the meaning of each column. From this file, TSS site information can be obtained.

2. Organize TSS Site Information

bedtools requires that the input file format be bed, gf, vcf, etc. Here we need to convert the downloaded original file to bed format, and the usage is as follows

awk '{print $3"\t"$5"\t"$5"\t"$2"\t"$1"\t"$4}' > hg38.tss.bed

The content is as follows

3. Run bedtools window

bedtools windows and intersect function is similar, are used to find the intersection of two intervals A and B, but window will add a custom length in the upstream and downstream of interval A, and then intersect with interval B, the principle is as follows

Take TSS upstream and downstream 5kb as an example, the usage is as follows

bedtools window -a hg39.tss.bed -b peak.bed -w 5000 -sm > overlap.txt

Through the window command, you can flexibly define the upstream and downstream intervals of TSS and quickly get the target gene corresponding to peak.

"How to use bedtools to predict the target gene of chip_seq data" is introduced here. Thank you for reading. If you want to know more about industry-related knowledge, you can pay attention to the website. Xiaobian will output more high-quality practical articles for everyone!