{
    "info": {
        "author": "Shiqi Tu",
        "author_email": "tushiqi@picb.ac.cn",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 4 - Beta",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
            "Operating System :: OS Independent",
            "Programming Language :: Python :: 2",
            "Programming Language :: Python :: 3",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
        ],
        "description": "=============================\nIntroduction to MAnorm2_utils\n=============================\n\n:Author: Shiqi Tu\n:Contact: tushiqi@picb.ac.cn\n:Version: 1.0.0\n:Date: 2018-08-24\n\n:code:`MAnorm2_utils` is designed to coordinate with MAnorm2_, an R package for\ndifferential analysis with ChIP-seq_ signals between two or more groups of\nreplicate samples. :code:`MAnorm2_utils` is primarily used for processing a set\nof ChIP-seq samples into a regular table recording the read abundances and\nenrichment states of a list of genomic bins in each of these samples.\n\n.. _MAnorm2: https://github.com/tushiqi/MAnorm2\n.. _ChIP-seq: https://en.wikipedia.org/wiki/ChIP-sequencing\n\n\nUsage\n------------------------------\n\nThe primary utility of :code:`MAnorm2_utils` comes from the two scripts bound\nwith it, named :code:`profile_bins` and :code:`sam2bed`, respectively.\n\n\nProfiling ChIP-seq signals in reference genomic regions\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n\nGiven the peak regions and mapping positions of reads of each of a set of\nChIP-seq_ samples, :code:`profile_bins` comes up with a list of reference\ngenomic bins (each being enriched for ChIP-seq signals in at least one of the\nsamples), and deduces the read count as well as enrichment status of each of\nthe bins in each sample. Refer to MACS_ for more information about the\ntechnical terms mentioned above.\n\n.. _MACS: https://genomebiology.biomedcentral.com/\n          articles/10.1186/gb-2008-9-9-r137\n\nWe recommend `MACS 1.4`_ for identifying peaks for ChIP-seq samples associated\nwith narrow genomic regions of reads enrichment (e.g., samples for most\ntranscription factors and histone modifications like H3K4me3 and H3K27ac). In\nfact, although having a general applicability, :code:`profile_bins` is\nspecifically suited to processing the output files generated by MACS 1.4. For\nhistone modifications constituting broad enriched domains (e.g., H3K9me3 and\nH3K27me3), we recommend SICER_ as the peak caller.\n\n.. _MACS 1.4: https://github.com/taoliu/MACS/downloads\n.. _SICER: https://academic.oup.com/bioinformatics/article/25/15/1952/212783\n\nThe following is a sample usage of :code:`profile_bins` of the simplest form:\n\n.. code:: bash\n\n   profile_bins --peaks=peak1.bed,peak2.bed \\\n                --reads=read1.bed,read2.bed \\\n                --labs=s1,s2 -n example\n\n.. Note::\n\n   :code:`profile_bins` only recognizes BED-formatted_ input files. For read\n   alignment results stored in SAM_ files, use first :code:`sam2bed` to\n   transform them into BED files before calling :code:`profile_bins` (BED files\n   created by :code:`sam2bed` have been specifically designed to suit\n   :code:`profile_bins`; see also the `section below`__). For BAM-formatted_\n   files, refer to Samtools_ for converting them into SAM files.\n\n.. _BED-formatted: BED_\n.. _BED: http://genome.ucsc.edu/FAQ/FAQformat.html#format1\n.. _BAM-formatted: SAM_\n.. _SAM: https://samtools.github.io/hts-specs/SAMv1.pdf\n.. _Samtools: https://www.htslib.org/\n__ `Transforming SAM into BED files`_\n\nIf everything goes smoothly, the command above will generate two files, named\n``example_profile_bins_log.txt`` and ``example_profile_bins.xls``,\nrespectively. The former records the full list of parameter settings for\ncalling :code:`profile_bins`, as well as some summary statistics regarding each\nof the supplied ChIP-seq samples. The latter gives the read count and\nenrichment status for each deduced reference genomic bin in each sample, and\nhas a format like the following (data shown here is only for illustration):\n\n.. table:: Example output of :code:`profile_bins`\n   :align: right\n\n   ======  =======  =======  ============  ============  =============  =============\n    chrom    start      end   s1.read_cnt   s2.read_cnt   s1.occupancy   s2.occupancy\n   ======  =======  =======  ============  ============  =============  =============\n     chr1    28112    29788           115             4              1              0\n     chr1   164156   166417           233           194              1              1\n     chr1   166417   168417           465           577              1              1\n     chr1   168417   169906            15            34              0              1\n   ======  =======  =======  ============  ============  =============  =============\n\nTo clarify, a genomic bin is \"occupied\" by a ChIP-seq sample if and only if its\nmiddle point is covered by some peak region of the sample.\n\n:code:`profile_bins` supports a number of parameters for a customized\nconfiguration for deducing reference genomic bins as well as counting the reads\nfalling in them. Type :code:`profile_bins --help` in the command line for a\ncomplete list of these parameters and a brief description of each of them.\nAmong others, several parameters deserve specific attention:\n\n- By default, :code:`profile_bins` merges peaks from all the provided ChIP-seq\n  samples into a consensus set of peak regions, and divides up each *broad*\n  merged peak into consecutive genomic bins. Specify :code:`--typical-bin-size`\n  to control the size of such genomic bins. Note that the merged peaks having a\n  size comparable to this parameter are left untouched.\n\n  The default value of :code:`--typical-bin-size`, which is 2000, suits well\n  the ChIP-seq samples of histone modifications. For ChIP-seq samples of\n  transcription factors, setting the parameter to 1000 is recommended.\n\n- In cases where summit positions of the supplied peaks are available (e.g.,\n  when the peaks are called by using `MACS 1.4`_), you may provide\n  :code:`profile_bins` with this information via specifying :code:`--summits`.\n  Summit positions will be used to determine an appropriate start point for\n  dividing up a broad merged peak.\n\n- Alternatively, you can directly specify a set of genomic regions as the\n  reference bins to profile, by setting :code:`--bins` to a BED_ file. In this\n  case, :code:`profile_bins` focuses on these provided bins and suppresses the\n  peak merging procedure.\n\n  :code:`--typical-bin-size` and :code:`--summits` are ignored when\n  :code:`--bins` is specified.\n\n- Before being assigned to reference bins, each read (or read pair) is\n  converted into a genomic locus representing the middle point of the\n  underlying DNA fragment. By default, :code:`profile_bins` treats the supplied\n  reads as single-end, and shifts downstream the 5' end of each of them by\n  :code:`--shiftsize` to reach the putative middle point. :code:`--shiftsize`\n  defaults to 100, and may be set to half of the practical DNA fragment size\n  selected in the library preparation process.\n\n- Set :code:`--paired` to indicate the reads are paired-end. In this case,\n  middle point of the underlying DNA fragment associated with each read pair\n  could be accurately inferred. Note that two reads from the same ChIP-seq\n  sample are considered as a read pair only if they have *exactly the same*\n  name (i.e., the 4th column in a BED_ file).\n\n  :code:`--shiftsize` is ignored when :code:`--paired` is set.\n\n- :code:`--keep-dup` controls the program's behavior regarding duplicate reads\n  (or read pairs) potentially resulting from PCR amplification. For single-end\n  reads, two reads are considered as duplicates if their 5' ends are mapped to\n  the same genomic locus; for paired-end reads, two read pairs are considered\n  as duplicates if their implied DNA fragments occupy the same genomic\n  interval.\n\n  By default, :code:`profile_bins` preserves all the reads (or read pairs) for\n  the counting procedure. For both paired-end reads and deep-sequencing\n  single-end reads, we strongly recommend setting :code:`--keep-dup` to 1 to\n  enhance the specificity of downstream analyses. In that case, for each\n  ChIP-seq sample only one read (or read pair) of a set of duplicates is\n  retained for counting. Note also that the output log file records, for each\n  sample, the ratio of reads (or read pairs) that are removed due to\n  :code:`--keep-dup`.\n\n- :code:`profile_bins` supports the idea of using a configuration file to\n  deliver parameters, to avoid repeated typing in the command line. To do that,\n  write a configuration file following the format as demonstrated below, and\n  pass it to :code:`--parameters`::\n\n    peaks=peak1.bed,peak2.bed\n    reads=read1.bed,read2.bed\n    labs=s1,s2\n    n=example\n    summits=summit1.bed,summit2.bed\n    paired\n    keep-dup=1\n\n  Note that :code:`--parameters` could be used in mixture with the other\n  command-line arguments.\n\nRefer to the `Manual of MAnorm2_utils`_ for a full specification of the\nparameters supported by :code:`profile_bins`.\n\n.. _Manual of MAnorm2_utils: https://github.com/tushiqi/MAnorm2_utils/\n                             tree/master/docs\n\n\nTransforming SAM into BED files\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n\n:code:`sam2bed` is designed to coordinate with :code:`profile_bins`, since the\nlatter only accepts BED-formatted_ files. The simplest form of calling\n:code:`sam2bed` is as follows:\n\n.. code:: bash\n\n   sam2bed -i File.sam -o File.bed\n\nThe program will read from the standard input stream if :code:`-i` is not\nspecified.\n\nIn the vast majority of cases, the default setting of most of the parameters\nsupported by :code:`sam2bed` should be used.\nThe only parameter that may be customized in\npractice is :code:`--min-qual`, which controls the program's behavior\nregarding filtering out the SAM_ alignment records with a low mapping quality.\nType :code:`sam2bed --help` in the command line for a brief description of each\nparameter supported by :code:`sam2bed`.\n\n\n\n\n\n\n",
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