dariober/SICERpy - Githubissues

NB This project is most likely superseded by epic; use that instead

SICERpy: A friendly version of SICER peak caller

SICER is a popular peak caller particularly suitable for detection of broad ChIP-Seq marks. However, I found the original master script, SICER.sh, clunky to use.

SICER.py is a re-write of SICER.sh aimed at improving the following aspects:

Friendly API SICER.py takes command line arguments using the usual and convenient format SICER.py --option arg. In contrast, the original script takes eleven (!) positional arguments. Also, each step of the pipeline is checked for clean exit so that if something goes wrong you now right away.
Input is BAM As opposed to SICER.sh which requires bed format. Options to filter reads by flag and mapping quality are also provided. To convert bed to bam see bedtools bedtobam
Parallel execution of multiple SICER runs The original script caused temporary files from multiple instances of SICER to overwrite each other. SICER.py instead uses unique temporary directories so it can be run in parallel in the same directory from the same input files.
Less redundant output By default, the only output produced is the table of candidate islands with their statistical significance.
Faster execution Some steps of the pipeline have been parallelised.

Requirements and Installation

SICER.py requires python 2.6+ with scipy package as per the original version. In addition it requires the pysam package.

To install, first download the SICERpy directory and change permission of SICER.py to be executable: chmod 755 SICER.py. Then use sicer in one of the following ways:

Best: Create a symlink from SICER.py to a directory somewhere on your PATH and execute SICER.py [options], e.g.

ln -s /path/to/SICERpy/SICER.py ~/bin/

Call using full path /path/to/SICERpy/SICER.py [options]
Add the whole directory SICERpy to your PATH variable.

Usage examples

These input files can be found in the ex/ directory.

SICER.py -t ex/test.bam -c ex/control.bam -rt 0 > peaks.bed 2> sicer.log

Here, the table of candidate islands is sent to peaks.bed. The log is captured by stderr. Note that by setting the redundancy threshold to 0 we use directly the input files without further filtering. This is useful if the bam file have been already de-duplicated with external tools like picard/MarkDuplicates.

Apply some filtering to discard reads with low mapping quality and with certain bits set (see explain samflag):

SICER.py -t ex/test.bam -c ex/control.bam -F 3972 -q 5 > peaks.bed

Important if working with paired-end reads discard the second-in-pair to avoid double counting!

The output is in bed format with columns:

chrom
start
end
ChIP island read count
CONTROL island read count
p value
Fold change
FDR threshold

The output file peaks.bed can be easily parsed to get the enriched regions. For example, the get regions with FDR < 0.01:

awk '$8 < 0.01' peaks.bed > peaks.01.bed

Help on options

The one shown here might be out of date

SICER.py -h
iusage: SICER.py [-h] [--treatment TREATMENT] --control CONTROL
                [--effGenomeSize EFFGENOMESIZE] [--requiredFlag REQUIREDFLAG]
                [--filterFlag FILTERFLAG] [--mapq MAPQ]
                [--redThresh REDTHRESH] [--windowSize WINDOWSIZE]
                [--gapSize GAPSIZE] [--fragSize FRAGSIZE] [--keeptmp]
                [--version]

DESCRIPTION

Run the SICER pipeline using a control and an input file.

SEE ALSO:

https://github.com/dariober/SICERpy

optional arguments:
  -h, --help            show this help message and exit
  --treatment TREATMENT, -t TREATMENT
                        Treatment (pull-down) file in bam format

  --control CONTROL, -c CONTROL
                        Control (input) file in bam format

  --effGenomeSize EFFGENOMESIZE, -gs EFFGENOMESIZE
                        Effective Genome as fraction of the genome size. It
                        depends on read length. Default 0.74.

  --requiredFlag REQUIREDFLAG, -f REQUIREDFLAG
                        Keep reads with these bits set in flag. Same as
                        `samtools view -f`. Default 0

  --filterFlag FILTERFLAG, -F FILTERFLAG
                        Discard reads with these bits set in flag. Same as
                        `samtools view -F`. Default 4.  You probably want to
                        discard also second-in-pair reads, secondary and
                        supplementary alignments, reads failing QC.

  --mapq MAPQ, -q MAPQ  Discard reads with mapping quality lower than this. Default 5.

  --redThresh REDTHRESH, -rt REDTHRESH
                        Redundancy threshold to keep reads mapping to the same
                        position on the same strand. Default 0 (do not filter
                        for redundancy). 

  --windowSize WINDOWSIZE, -w WINDOWSIZE
                        Size of the windows to scan the genome. WINDOW_SIZE is
                        the smallest possible island. Default 200.

  --gapSize GAPSIZE, -g GAPSIZE
                        Multiple of window size used to determine the gap size.
                        Must be an integer. Default: 3.

  --fragSize FRAGSIZE, -fs FRAGSIZE
                        Size of the sequenced fragment. The center of the the
                        fragment will be taken as half the fragment size.
                        Default 150.

  --keeptmp             For debugging: Do not delete temp directory at the end of run.

  --version             show program's version number and exit

TODO

Clean up the mess inside SICERpy. Lots of original code and scripts are not necessary anymore.
Handle cases where window size is larger than chrom size. Currently the solution is to create new genomes without the small chromosomes.
In fact, you don't need the genome data at all since it can be extracted from the bam header!
Re-write the other SICER*.sh scripts