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This article focuses on "how to use homer for peak annotations", interested friends may wish to take a look. The method introduced in this paper is simple, fast and practical. Let's let the editor take you to learn how to use homer to annotate peak.

Homer software integrates many functions, including peak calling, peak annotation, motif analysis and so on. Through this software, most of the analysis content of chip_seq can be completed, which is not too powerful. This article mainly introduces the use of peak annotations in this software.

Annotate peak through the script annotatePeaks.pl in homer, which is divided into the following two steps

1. Prepare annotated information for reference genomes

Homer has built-in annotated information for many species for download, and you can view all built-in species with the following command

Perl configureHomer.pl-list

The GENOMES part corresponds to the built-in supported species, and some of the contents are shown below

GENOMES

V5.10 hg19 v6.0 human genome and annotation for UCSC hg19

+ mm10 v6.0 mouse genome and annotation for UCSC mm10

-sacCer3 v6.0 yeast genome and annotation for UCSC sacCer3

-panTro5 v6.0 human genome and annotation for UCSC panTro5

Take hg19 as an example, download it as follows

Perl configureHomer.pl-install hg19

The downloaded information is saved in the data directory of the homer installation directory. Take hg19 as an example, in the data/genome/hg19 directory, the list of files is as follows

├── chr1.fa

├── chr2.fa

├── chr3.fa

├──... fa

├── chrom.sizes

├── conservation

├── hg19.annotation

├── hg19.aug

├── hg19.basic.annotation

├── hg19.full.annotation

├── hg19.miRNA

├── hg19.repeats

├── hg19.rna

├── hg19.splice3p

├── hg19.splice5p

├── hg19.stop

├── hg19.tss

├── hg19.tts

└── preparsed

Contains the fasta sequence of the reference genome and interval files of different regions.

The hg19.basic.annotation content is as follows

Intergenic chr1 1 10873 + N 1900000000

Promoter-TSS (NR_046018) chr1 10874 11974 + P 1

Non-coding (NR_046018, exon 1 of 3) chr1 11975 12227 + pseudo 125025

Intron (NR_046018, intron 1 of 2) chr1 12228 12612 + I 810684

Non-coding (NR_046018, exon 2 of 3) chr1 12613 12721 + pseudo 125026

Intron (NR_046018, intron 2 of 2) chr1 12722 13220 + I 810684

Non-coding (NR_046018, exon 3 of 3) chr1 13221 13361 + pseudo 125027

At the same time, there are gene annotation files corresponding to the reference genome in the data/accession directory.

Human2gene.tsv records the ubigene id, gene symbol and other information of the gene, as shown below.

ADE73044 3107 Hs.656020 NM_002117 ENSG00000204525 HLA-C

ENSG00000113163 10087 Hs.270437 NM_005713 ENSG00000113163 COL4A3BP

DB065460 9947 Hs.132194 NM_005462 ENSG00000155495 MAGEC1

ENSP00000282466 285313 Hs.58561 NM_178822 ENSG00000152580 IGSF10

DB029361 22849 Hs.131683 NM_014912 ENSG00000107864 CPEB3

XP_016877211 87 Hs.235750 NM_001102 ENSG00000072110 ACTN1

EAW77897 56965 Hs.270244 NM_020213 ENSG00000137817 PARP6

Human.description records list the functional description, category and other information of the gene, as shown below

two。 Make a comment

The usage is as follows

AnnotatePeaks.pl peak.bed hg19 > peak.annotation.xls

The first parameter is the bed file of peak, and the second parameter is the name of the reference genome. The output is as follows

The annotation consists of two parts: the first part is the transcription initiation site TSS which is closest to the peak interval, and the second part is about the distribution of peak in the genome region, such as TSS,TTS,3'UTR,5'UTR and other regions.

At this point, I believe you have a deeper understanding of "how to use homer for peak annotations". You might as well do it in practice. Here is the website, more related content can enter the relevant channels to inquire, follow us, continue to learn!

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