Broad Peak Calling Tool -- SICER

更新，记录如何添加新的基因组

FIRST, important!

1. create new enviroment

    conda create -n SICER2 python=3.6

    note! SICER2 need python3.

    conda activate new_env

NEXT

2. download:

   git clone https://github.com/zanglab/SICER2.git

   pip install SICER2

   link:  https://github.com/zanglab/SICER2

3. Adding your own species(添加新的基因组):

    'GenomeData.py', this file lie in  where you 'git clone', path:SICER2/sicer/lib/GenomeData.py

      git clone https://github.com/zanglab/SICER2.git

3.1 进入到已克隆的文件夹下面修改  GenomeData.py，如下图所示

添加染色体信息

note:Create a list of all the chromosome numbers like "hg38_chroms",

            Create a dictionary that maps chromosome numbers to their length like "hg38_chrom_lengths",

            Update both "species_chroms" and "species_chrom_lengths" .

           Use the species name used as key value in "species_chroms" and "species_chrom_lengths" as argument for "--species".

添加染色体长度信息 添加到参考基因组信息中

Do not forget:

pip install -e .

    note:In the top directory of the repo (include setup.py), executive command.

4. call peaks:

-t/--treatment_file (Required). The file must either be in BED or BAM format (note that you need bedtools installed to directly enter BAM files). The file name can either the relative path or the absolute path of the file.

-c/--control_file (Optional). Like the treatment file, control file must be in BED or BAM format and can be the relative path or the absolute path of the file. -s/--species (Required). ex)

-s hg38 -rt/--redundancy_threshold (Optional). The number of copies of indentical reads allowed in a library. Default value is 1.

-w/--window_size (Optional). Resolution of SICER. Default value is 200 (bp)

-f/--fragment_size (Optional). The amount of shift from the beginning of a read to the center of the DNA fragment represented by the read. Default value is 150 (bp).

-egf/--effective_genome_faction (Optional). Effective genome as fraction of the genome size. Default value is 0.74.

-fdr/--false_discovery_rate (Optional). Remove all islands with an false-discovery-rate below cutoff. Default value is 0.01.

-g/--gap_size (Optional). The minimum length of a "gap" such that neighboring window is an "island." Please note that this value must be a multiple of the window size. Default value is 600 (bp).

-e/--e_value (Optional). E-value. Requires user input when no control library is provided. Default value is 1000

-o/--output_directory (Optional). Path of the directory in which results will be stored. Default output directory is the current working directory.

For example:

sicer -t treatment.bed -c control.bed -s hg38 -w 200 -rt 1 -f 150 -egf 0.74 -fdr 0.01 -g 600 -e 1000 --significant_reads