Mercurial > repos > jeremyjliu > region_motif_enrichment
changeset 22:85ad03e5be67 draft
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| author | jeremyjliu |
|---|---|
| date | Wed, 12 Nov 2014 15:33:11 -0500 |
| parents | 2c909bfdd090 |
| children | d3e4ce1698b9 |
| files | README.md region_motif_db/pouya_test_dir/AP-1_disc1_8mer.RData region_motif_db/pouya_test_dir/AP-1_disc1_8mer_C1.RData region_motif_db/pouya_test_dir/AP-1_disc1_8mer_C10.RData region_motif_db/pouya_test_dir/AP-1_disc1_8mer_C2.RData region_motif_db/pouya_test_dir/AP-1_disc1_8mer_C3.RData region_motif_db/pouya_test_dir/AP-1_disc1_8mer_C4.RData region_motif_db/pouya_test_dir/AP-1_disc1_8mer_C5.RData region_motif_db/pouya_test_dir/AP-1_disc1_8mer_C6.RData region_motif_db/pouya_test_dir/AP-1_disc1_8mer_C7.RData region_motif_db/pouya_test_dir/AP-1_disc1_8mer_C8.RData region_motif_db/pouya_test_dir/AP-1_disc1_8mer_C9.RData region_motif_db/pouya_test_dir/ZNF263_disc1_8mer.RData region_motif_db/pouya_test_dir/ZNF263_disc1_8mer_C1.RData region_motif_db/pouya_test_dir/ZNF263_disc1_8mer_C2.RData region_motif_db/pouya_test_dir/ZNF263_disc1_8mer_C3.RData region_motif_db/pouya_test_dir/ZNF263_disc1_8mer_C4.RData |
| diffstat | 17 files changed, 0 insertions(+), 204 deletions(-) [+] |
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--- a/README.md Wed Nov 12 15:25:44 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,204 +0,0 @@ -# Region-Motif-Compare Tools -Version 1.1 Released 2014 -Park Laboratory -Center for Biomedical Informatics -Harvard University - -Contact -Jeremy Liu (jeremy.liu@yale.edu) -Nils Gehlenborg (nils@hms.harvard.edu) - -## Overview -### Structure -The tool suite consists of: - -1. Two Rscripts: region_motif_compare.r and region_motif_intersect.r -2. Two Xml Files: region_motif_compare.xml and region_motif_intersect.xml -3. Motif Database Directory: region_motif_db -4. Dependency Library Directory: region_motif_lib -5. Galaxy Workflows: Files with suffix ".ga" that can be imported into the local -Galaxy instance after installation of the tool. - -### Description -1. **region_motif_intersect.r** (1 bed -> 1 tsv): -Takes one bed file of regions as input. Then it calculates -the number of intersections of the regions and the motifs. region_motifs_intersect.r -outputs a tab separated values (tsv) file of motif names and intersection counts. -**Important Note:** region_motif_intersect.r makes no assumptions about the nature -of the input regions. For example, if overlapping regions are inputted, motifs that -intersect the overlap will be double counted. Thus, it is recommended that regions -be merged before using this tool, using the merge tool in the Galaxy toolshed. - -2. **region_motif_compare.r** (2 tsv -> 2 tsv & 1 png): -Takes as input two tsv files of motifs / regions intersection -counts. These generally originate from running region_motif_intersect.r on two sets -of different regions with the same query motif database. Based on the counts, -region_motif_compare.r then determines the enrichment (or depletion) of certain -motifs across the two regions. This is done by a correcting for the size and gc -content of the region, and applying a Poisson test to the counts. -Then, region_motif_compare.r outputs the most significant enriched or depleted -motifs as a tsv. In addition, the tool outputs a diagnostic plot containing -graphical representations of the motif counts, gc correction curves, and significant -motifs that distinguish the two regions (selected via p value). - -3. **region_motif_db**: Contains motif positions as compressed, indexed tabix files. - -4. **region_motif_lib**: Contains dependencies (i.e. plotting.r) for region_motif_compare.r - -## Installation -Directions for installing the region-motif-compare tools into a personal computer -and a local Galaxy instance. - -1. Follow the online directions to install a local instance of Galaxy (getgalaxy.org). -Optionally, follow the directions to install Refinery (refinery-platform.readthedocs.org) - -2. Clone the github repository to your local computer - ```` - git clone https://github.com/parklab/refinery-galaxy-tools.git - cd refinery-galaxy-tools/region-motif-compare - ```` - -3. Make a directory for the tools in Galaxy instance. This serves as a category -for the tool in the tools sidebar. You can also place the tools in an existing -or alternatively named directory, but remember to update tool_conf.xml to reflect this. - ```` - cd ~/galaxy-dist/tools/ - mkdir my_tools - cd my_tools - ```` - -4. Copy over ".r" and ".xml" files, as well as `region_motif_db` and `region_motif_lib` - ```` - cd refinery-galaxy-tools/region-motif-compare - cp *.r ~/galaxy-dist/tools/my_tools - cp *.xml ~/galaxy-dist/tools/my_tools - cp -r region_motif_db ~/galaxy-dist/tools/my_tools - cp -r region_motif_lib ~/galaxy-dist/tools/my_tools - ```` - -5. Edit `~/galaxy-dist/tool_conf.xml` to reflect the addition of the new tools. -Add the following lines within the `<toolbox>` tags. If in Step 3 you copied -the tools to a different directory than `my_tools`, edit the code snippet -to reflect the correct path name. - ```` - <section id="mTools" name="My Tools"> - <tool file="my_tools/region_motif_intersect.xml" /> - <tool file="my_tools/region_motif_compare.xml" /> - </section> - ```` - -6. Download the motif databases and place them into `region_motif_db` - ```` - cd ~/galaxy-dist/tools/my_tools/region_motif_db - wget ????/pouya_motifs.bed.bgz - wget ????/pouya_motifs.bed.bgz.tbi - wget ????/jaspar_jolma_motifs.bed.bgz - wget ????/jaspar_jolma_motifs.bed.bgz.tbi - wget ????/mm9_motifs.bed.bgz - wget ????/mm9_motifs.bed.bgz.tbi - ```` - -7. Install the Bioconductor R package Rsamtools for dealing with tabix files - ``` - $ R - > source("http://bioconductor.org/biocLite.R") - > biocLite("Rsamtools") - ```` - -8. If in Step 3 you copied the tools to an existing directory or an alternatively -named directory, you must edit the following file paths. - In `region_motif_intersect.r` and `region_motif_compare.r` edit `commonDir`: - ```` - # Replace this line - commonDir = concat(workingDir, "/tools/my_tools") - # With this edited line - commonDir = concat(workingDir, "<relative_path_from_galaxy_root>/<tool_directory>") - ```` - In addition, edit `region_motif_intersect.xml` and `region_motif_compare.xml` to - reflect the path of the tools relative to the galaxy root directory. - ```` - <command interpreter="bash"> - /usr/bin/R --slave --vanilla -f $GALAXY_ROOT_DIR/<path_to_tools>/region_motif_intersect.r --args $GALAXY_ROOT_DIR $db_type $in_bed $out_tab - </command> - ```` - ```` - <command interpreter="bash"> - /usr/bin/R --slave --vanilla -f $GALAXY_ROOT_DIR/<path_to_tools>/region_motif_compare.r --args $GALAXY_ROOT_DIR $db_type $in_tab_1 $in_tab_2 $out_enriched $out_depleted $out_plots - </command> - ```` - -## Running the Tools -### Running from Galaxy -1. To run the tools as workflows, import the .ga workflows included in the github -via the Galaxy workflow user interface. Then, upload and select two input BED files. - -2. To run the tools individually, select the tool from the tools toolbar, provide -a BED file (Region Motif Intersect) or two tsv files (Region Motif Compare), and -select a query database from the dropdown menu. - -### Running from Refinery -1. Import the .ga workflows into a local Galaxy instance. These workflows have -already been annotated for Refinery. - -2. Add the local Galaxy instance to the Refinery installation. - ```` - python manage.py create_workflowengine <instance_id> "<group_name>" - ```` - -3. Import the Galaxy workflows into Refinery. - ```` - python manage.py import_workflows - ```` -4. Run the tools from the Refinery user interface. - -### Running as Command Line Tools -You can also run the tools from the command line, an example of which is shown below. -More information is found in the headers of the r source files. -```` -cd ~/galaxy-dist/tools/my_tools -R --slave --vanilla -f region_motif_intersect.r --args ~/galaxy-dist p <path_to_bed_file> <path_to_output_tsv> -R --slave --vanilla -f region_motif_compare.r --args ~/galaxy-dist p <path_to_region1_counts> <path_to_region2_counts> <enriched_motifs_output_tsv> <depleted_motifs_output_tsv> <plots_png> -```` - -## Interpreting Results -### Motif Database and Result Notation -TF motif positions for hg19 and mm9 were curated from three databases: -ENCODE TF motif database "Pouya" (http://compbio.mit.edu/encode-motifs/) -JASPAR database "Jaspar" (http://jaspar.genereg.net/) -DNA binding specificities of human transciption factors "Jolma" (http://www.ncbi.nlm.nih.gov/pubmed/23332764) - -For ENCODE TF motifs, the genomic locations were taken straight from the database. -In addition, position weight matrices (pwms) were obtained by averaging the -sites in the genome for a motif. These are labeled with "\_8mer\_". -Fake motifs were also generated, by shuffling the pwms of actual motifs and -mapping to the genome and are labeled with "_8mer_C". - -For JASPAR and Jolma motifs, mast was run to determine genomic locations from the -provided pwms. The motif alignmment thresholds were set to the top 5k, 20k, 100k, and -250k sites and the redundant maps removed with the top 30k sites have the same score. -These are labeled with "_t5000" and likewise. - - -## Motif Tabix File Creation -Starting with a BED file of motif positions (minimal chr, start, end), follow -below to generate a tabix file that can be placed in `region_motif_db` and -used by the tools. - -1. Download Tabix (http://sourceforge.net/projects/samtools/files/tabix/) and install. -Add `tabix` and `bgzip` binaries to your file path. - ```` -tar -xvjf tabix-0.2.6.tar.bz2 -cd tabix-0.2.6 -make - ```` - -2. Construct bgzip files and index files. - ```` -cd ~/galaxy-dist/tools/my_tools/region_motif/db -(grep ^"#" jaspar_motifs.bed; grep -v ^"#" jaspar_motifs.bed | sort -k1,1 -k2,2n) | bgzip > jaspa_motifs.bed.bgz -tabix -p bed jaspar_motifs.bed.bgz # this generates jaspar_motifs.bed.bgz.tbi - ```` - -3. Add the path to `jaspar_motifs.bed.bgz` to the selection options for the variable -`motifDB` in `region_motif_intersect.r` and `region_motif_compare.r`. To enable -the new database in Galaxy, you will have to edit the xml files for both tools.