How to apply tagAlign format in MACS Software

This article is to share with you about the use of tagAlign format in MACS software, the editor thinks it is very practical, so I share it with you to learn. I hope you can get something after reading this article.

When using macs for peak calling, you can import a BED file in addition to the BAM/SAM file corresponding to the sample. We are all very familiar with BAM files, which can be produced by comparing the sequences to the genome, and the various alignment software also supports the output BAM/SAM format. The file in this format records the sequence alignment, and the sequence depth distribution on the genome can be calculated according to this file, so as to compare the distribution of different samples for peak calling, so what about the BED file?

In BAM files, the core information is the correspondence between sequences and genomic regions, that is, which regions of the genome are aligned by those sequences. This information can also be recorded through BED format. The function of bamtobed is also provided in bedtools, and the basic usage is as follows

Bedtools bamtobed-I input.bam > out.bed

The output is shown below

The first three columns represent the chromosome position on the reads alignment, the fourth column represents the name of the reads, the fifth column represents the quality value MAPQ of the alignment, and the sixth column represents the positive and negative chain information.

This six-column BED file is named tagAlign format in ENCODE. For a detailed explanation, see the link below.

Https://genome.ucsc.edu/FAQ/FAQformat.html#format13

For double-ended sequenced data, there is also a special bed format-bedpe, which is used as follows

Bedtools bamtobed-I input.bam-bedpe > out.bed

The content is as follows

The bedpe format shows the alignment of the R1 and R2 reads in one line, with 10 columns.

For single-ended sequences. It is OK to use bed format directly; for double-end education, bedpe format is recommended. Both formats can be called tagAlign and can be used as input files for macs.

Macs2 callpeak\

-t ip.bedpe\

-c input.bedpe\

-- outdir out_dir\

-n chip\

-g hs

TagAligen format compared to bam, the file size will be much smaller, more convenient to read files.

The above is how the tagAlign format is used in MACS software. The editor believes that there are some knowledge points that we may see or use in our daily work. I hope you can learn more from this article. For more details, please follow the industry information channel.