Home - JSuryatenggara/ChIP-AP GitHub Wiki

Welcome to the ChIP-AP wiki!

ChIP-AP is now published! Check it out here: https://academic.oup.com/bib/advance-article/doi/10.1093/bib/bbab537/6489109

From here (and on the right) you will find the different guides and tutorials for different aspects of ChIP-AP from detailed setup, to Q&A's and guides on interpreting ChIP-AP's output directory structure.

For an overview of ChIP-AP, refer to our guide.

For VERY detailed documentation of ChIP-AP's outputs and the inner workings of this beast, refer to the documentation wiki.

Installation instructions for advanced users can be found on the github's main page. Those found here are detailed step-by-step instructions with screenshots for users to set up ChIP-AP on modern OS'es who require a little extra support to get things running. If you run into issues while installing, this will almost certainly be because of previous configurations that are disrupting the installation process. While it'd be great if we can cater to every installation support request, unfortunately we cant as its only 2 of us and not a team supporting ChIP-AP. Do your best using Google to find a solution but if you're really stuck drop an issue request and we'll see what we can do to try and sort you out.

  • For installing ChIP-AP on Windows 10 and Windows 11 (yes Windows!!!), the wiki can be found here.
  • For installing ChIP-AP on MacOS (Works on both Intel Macs and Apple-Silicon Macs), the wiki can be found here.
  • For installing ChIP-AP on Linux (Only Ubuntu based editions have been tested), the wiki can be found here.
  • For installing ChIP-AP in a VirtualMachine Environment, refer to our VM wiki.

If you have a question and cannot find the answer to it in the Q&A, drop us a line by email or submit an issue request above (with the right label) and we'll get back to you as soon as we can although give the documentation a thorough read-through as we have addressed a great many questions we anticipated we would be getting already.

Good luck using ChIP-AP folks!!!

And don't forget - please be kind rewind!

Version Update Changelogs

Version 4.1

  • Published version of ChIP-AP. First version to be released on GitHub.

Version 5.0

  • Second version to be released on GitHub.
  • Peak type "unsure" is now available as an optional argument for the --peak flag.
    • When peak type is "unsure", ChIP-AP will run twice, sequentially, not altogether.
    • First run with narrow peak type settings. Second run with broad peak type settings.
    • Results and other files will be stored in folder [setname]_narrow and [setname]_broad
    • The same settings table will be used for both runs.
  • Motif enrichment analysis by HOMER and MEME are now integrated into ChIP-AP.
    • ChIP-AP now is able to run motif enrichment analysis based on the consensus and/or union sets of the detected peaks
    • HOMER's findMotifsGenome.pl module performs the first motif enrichment analysis
      • Only available when processing narrow peaks dataset (--peak narrow)
      • Will be performed when user includes --homer_motif [consensus/union/both] flag argument in ChIP-AP command line
      • The results will be stored in a new folder 24_homer_motif_enrichment
    • MEME's meme-chip module performs the second motif enrichment analysis
      • Only available when processing narrow peaks dataset (--peak narrow)
      • Will be performed when user includes --meme_motif [consensus/union/both] flag argument in ChIP-AP command line
      • The results will be stored in a new folder 25_meme_motif_enrichment
  • fold_change_calculator_suite_3.0.py replaces fold_change_calculator_suite_2.1.py
    • Now adds each replicate's peak center coordinate into the resulting file: setname_all_peaks_calculated.tsv
    • Weighted peak center coordinate for narrow peak type, and simply peak mid-point coordinate for broad peak type
    • Weighted peak center coordinate value is needed for the new script meme_sequence_extractor_5.0.py
  • A home-made script meme_sequence_extractor_5.0.py is added into the pipeline
    • Needed for automated preparation of meme-chip FASTA-formatted target and background inputs
    • Recognizes and processes multiple replicates separately (based on each weighted peak center coordinate). meme-chip then follows up by processing each replicate separately, generating respective results for each replicate
    • Only when ChIP and control aligned reads (.bam) are not merged or force-merged
  • chipap_dashboard_2.0.py replaces the older chipap_dashboard.py (1.0)
    • Now supports unsure peak type
    • Now supports motif enrichment analysis by HOMER and MEME
    • Now supports real time detection of manually typed-in sample table, settings table, and known motifs file
  • chipap_wizard_2.0.py replaces the older chipap_wizard.py (1.0)
    • Now supports unsure peak type
    • Now supports motif enrichment analysis by HOMER and MEME
    • Now supports real time detection of manually typed-in sample table, settings table, and known motifs file
    • A few minor tweaks on the data inputting flow
  • For consistencies in codes between different versions of scripts, versions are removed from script file name. Additionally, the wording "suite" in several scripts does not really make sense, so we removed them.
    • chipap_v5.0.py --> chipap.py
    • Genrich_1.0.py --> Genrich.py
    • fold_change_calculator_suite_3.0.py --> fold_change_calculator.py
    • meme_sequence_extractor_5.0.py --> meme_sequence_extractor.py
    • GO_annotate_suite_1.1.py --> GO_annotator.py
    • pathway_annotate_suite_1.1.py --> pathway_annotator.py
    • peak_caller_stats_suite.py --> peak_caller_stats_calculator.py
    • chipap_dashboard_2.0.py --> chipap_dashboard.py
    • chipap_wizard_2.0.py --> chipap_wizard.py
  • File default_settings_table has been renamed to default_settings_table.tsv
    • To better reflect its table format
  • Software update check implemented at the beginning of pipeline.
    • Informing users of newer version of ChIP-AP script(s) available on GitHub.

Version 5.1

  • Third version to be released on GitHub
  • Peak reproducibility (IDR) calculations are now intergrated into ChIP-AP pipeline
    • Using the IDR module, calculates IDR value of each peak in the full peak list: dataset_name_all_peaks_calculated.tsv
  • Reads aligned chr_alt, chr_fix, chrN_random, chrUn, and chrM in externally aligned .bam files are now properly filtered out

Version 5.2

  • Fourth version to be released on GitHub
  • ChIP-AP is now published in Briefings in Bioinformatics! Check our paper to get more insight on how it can be very useful for your ChIP-seq!
  • Fixed a bug in GEM peak caller where ChIP and control files flags and arguments sometimes are buggy when multiple replicates are involved
  • 'overwrite=t' is added to bbduk.sh command line to allow overwriting if any of its output file already exist
  • Fixed a bug in script Genrich.py where ChIP and control files flags and arguments sometimes are buggy when -adjustp flag is not in use

Version 5.3

  • Fifth version to be released on GitHub
    • Fixed issue where GEM was given a non-integer value for its -t flag argument

Version 5.4

  • Sixth version to be released on GitHub
    • --fcmerge flag will now automatically be activated when the number of ChIP samples are unequal to control samples without requiring any user prompt.
  • chipap_installer.py now works for anaconda installed under a different parent directory name other than “anaconda3”
    • Upon not finding “anaconda3” parent directory name, the installer will attempt to recognize the actual parent directory name, in which file bin/conda is located.
    • As a failsafe measure, upon still being unable to find anaconda parent directory, the installer will prompt the user to manually key in the full path to anaconda parent directory, before proceeding with the installation.
  • The .yaml files for ChIP-AP installation have been updated
    • The R version the line “r-base=3.2.2=0” trying to install cannot be found anymore in anaconda. To fix this issue, and possibly similar issues in the future, the line has now been simplified to be able to flexibly find and install any compatible R version:
      • “r-base=3.2.2=0” changed to “r”
  • default_settings_table.tsv has been updated
    • Due to the prevalence of Illumina NGS in the field, the default arguments for adapter trimming by BBDuk has been changed to better trim read-through adapter sequences at the 3’ end of reads:
      • “ktrim=l hdist=2” changed to “ktrim=r k=21 mink=8 hdist=2 hdist2=1”