Tool: Tool to annotate ChIP-Seq peaks (hg19 or mm10) and find neighboring peaks from multiple experiments.

Wrote this c++ tool for internal use in our lab for some of our custom analysis, thought it might be a good idea to share it with the community.

It's a simple program to annotate human hg19 or mouse mm10 aligned ChIP-Seq peak files. This tool also takes multiple ChIP-Seq peak files from different experiments and finds neighbors of the primary peak file and annotate it.

The tool will parse the gencode annotation database file and list(s) of ChIP-Seq peaks in bed file format. Report detailed promoter / gene-body / intergenic / enhancer occupancy in human or mouse.

Multi peak option reports neighboring peaks in order to elicit co-acting transcription factors. For e.g. With this feature you can correlate your peaks with ENCODE ChIP-Seq data or multiple related ChIP-Seq data-sets.

Compiling:

gunzip gencode.v19.annotation.gtf.gz
gunzip enhancers.bed.gz
make

Running:

20GB RAM required on Linux

Single peak file:

./peak_tool_multi ./test.bed > test.genes.txt

Output:

chr1 1778750 MACS_peak_51 102.12 INTRON GNB1 - GNB1-001 protein_coding 1822495 43745
chr1 1933483 MACS_peak_57 93.87 INTRON C1orf222 - C1orf222-007 retained_intron 1935276 1793
chr1 3446145 MACS_peak_91 85.75 INTRON MEGF6 - MEGF6-001 protein_coding 3448012 1867
chr1 4003155 MACS_peak_104 58.09 ENHANCER . . . . . .
chr1 5787471 MACS_peak_121 1325.16 INTERGENIC . . . . . .
chr1 6473142 MACS_peak_138 988.16 EXON HES2 - HES2-002 protein_coding 6484730 11588
chr1 7259083 MACS_peak_154 60.32 INTRON CAMTA1 + CAMTA1-001 protein_coding 6845384 413699
chr1 8031408 MACS_peak_181 750.45 EXON PARK7 + PARK7-004 protein_coding 8014351 17057
chr1 8319346 MACS_peak_195 3100 ENHANCER . . . . . .

The output is in the following format

chrnum peak_mid peak_name peak_score peak_location gene_name strand isoform isoform_coding_type tx_start_site distance_tss

Multiple peak files:

./peak_tool_multi EXP1.bed EXP2.bed EXP3.bed EXP4.bed > EXP1_EXP2_EXP3_EXP4.genes.txt

Output:

chr1 714304 MACS_peak_2 158.84 INTERGENIC . . . . . . 714017 MACS_peak_1 68.78 -287 . 714039 MACS_peak_1 170.93 -265 . 714023 MACS_peak_1 245.28 -281 .
chr1 769360 MACS_peak_8 421.42 INTERGENIC . . . . . . 769283 MACS_peak_3 55.43 -77 . 769273 MACS_peak_5 154.26 -87 . 769292 MACS_peak_3 71.24 -68 .
chr1 840155 MACS_peak_10 96.66 INTERGENIC . . . . . . 840097 MACS_peak_6 165.5 -58 . 840026 MACS_peak_11 57.72 -129 . 840075 MACS_peak_8 134.82 -80 .
chr1 840738 MACS_peak_11 137.93 ENHANCER . . . . . . 840097 MACS_peak_6 165.5 -641 . 840026 MACS_peak_11 57.72 -712 . 840075 MACS_peak_8 134.82 -663 .
chr1 911680 MACS_peak_15 241.99 PROMOTER C1orf170 - C1orf170-002 retained_intron 912021 341 911740 MACS_peak_20 271.3 60 281 911707 MACS_peak_31 285.65 27 314 911709 MACS_peak_23 251.1 29 312
chr1 994706 MACS_peak_18 95.46 ENHANCER . . . . . . 994613 MACS_peak_35 66.76 -93 . 995290 MACS_peak_52 57.49 584 . 994655 MACS_peak_37 61.84 -51 .
chr1 1003263 MACS_peak_19 71.56 INTERGENIC . . . . . . 1003034 MACS_peak_37 252.84 -229 . 1003088 MACS_peak_54 281.96 -175 . 1003078 MACS_peak_39 643.19 -185 .
chr1 1003982 MACS_peak_20 104.28 ENHANCER . . . . . . 1003034 MACS_peak_37 252.84 -948 . 1003088 MACS_peak_54 281.96 -894 . 1003078 MACS_peak_39 643.19 -904 .
chr1 1098334 MACS_peak_23 149.14 INTERGENIC . . . . . . 1098987 MACS_peak_50 185.58 653 . 1098482 MACS_peak_70 130.48 148 . 1098535 MACS_peak_51 138.52 201 .

chip-seq

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updated 3.9 years ago by Ram

• written 10.9 years ago by abhishek.mitra •

1 answer

Hi, Did you have an article on this tool? I would like to receive the source of enhancer list for mm10 and what the different between two of them (enhancers-mm10.bed, super-enhancers-mm10.bed)? Thank,

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written 10.3 years ago by tamars •

I used mouse enhancer data from: http://chromosome.sdsc.edu/mouse/download.html

Super enhancers are from http://bioinfo.au.tsinghua.edu.cn/dbsuper/ses.php?genome=hg19&cell_type=C_001

You may switch the enhancers bed files with your own annotation of enhancers which might be more suitable for your case, and the tool will automatically annotate.

Thank you!

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written 10.3 years ago by abhishek.mitra •

Hi, Abhishek:

I tried to use the peak-tool and got the output correctly. But I noticed all the INTERGENICE and ENHANCER, ENHANCER-SUPER did not have the correlate gene, distance to TSS, but the PROMOTER annotation has all this information, did you have way to add these information? Thanks.

chr1 10162 H3K27Ac_Dox_peak_1 69 INTERGENIC . . . . . . chr1 13995 H3K27Ac_Dox_peak_2 45 INTERGENIC . . . . . . chr1 29571 H3K27Ac_Dox_peak_3 380 INTERGENIC . . . . . . chr1 323229 H3K27Ac_Dox_peak_4 40 INTERGENIC . . . . . . chr1 442492 H3K27Ac_Dox_peak_5 152 INTERGENIC . . . . . . chr1 540745 H3K27Ac_Dox_peak_6 106 ENHANCER . . . . . . chr1 668941 H3K27Ac_Dox_peak_7 67 INTERGENIC . . . . . . chr1 672980 H3K27Ac_Dox_peak_8 78 INTERGENIC . . . . . . chr1 714250 H3K27Ac_Dox_peak_9 229 INTERGENIC . . . . . . chr1 762728 H3K27Ac_Dox_peak_10 251 ENHANCER-SUPER . . . . . . chr1 840330 H3K27Ac_Dox_peak_11 64 ENHANCER-SUPER . . . . . . chr1 894324 H3K27Ac_Dox_peak_12 152 PROMOTER KLHL17 + KLHL17-001 protein_coding 895967 -1643 chr1 894324 H3K27Ac_Dox_peak_12 152 PROMOTER NOC2L - NOC2L-001 protein_coding 894670 346 chr1 896136 H3K27Ac_Dox_peak_13 112 PROMOTER KLHL17 + KLHL17-001 protein_coding 895967 169

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written 8.3 years ago by lhaiyan3