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Add sections to README on how to create a cisTarget track database.
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Add sections to README on how to create a cisTarget track database.
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@ghuls
ghuls committed Dec 12, 2022
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Expand Up @@ -171,6 +171,7 @@ When running the scripts in this repo, you might need around 3 times the amount
| script | description |
|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------:|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| [`create_cistarget_motif_databases.py`](#create_cistarget_motif_databasespy) | Create cisTarget motif databases. |
| [`create_cistarget_track_databases.py`](#create_cistarget_track_databasespy) | Create cisTarget track databases. |
| [`combine_partial_motifs_or_tracks_vs_regions_or_genes_scores_cistarget_dbs.py`](#combine_partial_motifs_or_tracks_vs_regions_or_genes_scores_cistarget_dbspy) | Combine partial cisTarget motifs or tracks vs regions or genes scores databases to: **1)** a complete cisTarget motifs or tracks regions or genes scores database and **2)** a complete cisTarget regions or genes vs motifs or tracks scores database. |
| [`combine_partial_regions_or_genes_vs_motifs_or_tracks_scores_cistarget_dbs.py`](#combine_partial_regions_or_genes_vs_motifs_or_tracks_scores_cistarget_dbspy) | Combine partial cisTarget regions or genes vs motifs or tracks scores databases to: **1)** a complete cisTarget regions or genes vs motifs or tracks scores database and **2)** a complete cisTarget motifs or tracks vs regions or genes scores database. |
| [`convert_motifs_or_tracks_vs_ regions_or_genes_scores_to_ rankings_cistarget_dbs.py`](#convert_motifs_or_tracks_vs_regions_or_genes_scores_to_rankings_cistarget_dbspy) | Convert cisTarget motifs or tracks vs regions or genes scores database to cisTarget rankings database. |
Expand Down Expand Up @@ -255,6 +256,60 @@ options:
```
#### create_cistarget_track_databases.py
```bash
❯ ${create_cistarget_databases_dir}/create_cistarget_track_databases.py --help
usage: create_cistarget_track_databases.py [-h] -b BED_FILENAME -T TRACKS_DIR -d TRACKS_LIST_FILENAME
-o DB_PREFIX [-a BIGWIG_AVERAGE_OVER_BED_PATH]
[-t NBR_THREADS] [-p CURRENT_PART NBR_TOTAL_PARTS]
[-g EXTRACT_GENE_ID_FROM_REGION_ID_REGEX_REPLACE] [-s SEED]
[-r SSH_COMMAND]

Create cisTarget track databases.

options:
-h, --help show this help message and exit
-b BED_FILENAME, --bed BED_FILENAME
BED filename which contains the regions/genes to score with
bigWigAverageOverBed for each bigwig track (ChIP-seq) files.
-T TRACKS_DIR, --tracks_dir TRACKS_DIR
Path to directory with bigwig track (ChIP-seq) files.
-d TRACKS_LIST_FILENAME, --tracks TRACKS_LIST_FILENAME
Filename with list of track IDs to be scored from directory specified by "--
tracks_dir".
-o DB_PREFIX, --output DB_PREFIX
Feather database prefix output filename.
-a BIGWIG_AVERAGE_OVER_BED_PATH, --bwaob BIGWIG_AVERAGE_OVER_BED_PATH
Path to bigWigAverageOverBed
(http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/bigWigAverageOverBed).
Default: "bigWigAverageOverBed".
-t NBR_THREADS, --threads NBR_THREADS
Number of threads to use when scoring tracks. Default: 1.
-p CURRENT_PART NBR_TOTAL_PARTS, --partial CURRENT_PART NBR_TOTAL_PARTS
Divide the tracks list in a number of total parts (of similar size) and score
only the part defined by current_part. This allows creating partial databases
on machines which do not have enough RAM to score all tracks in one iteration.
This will only create a partial regions/genes vs tracks scoring database ({db_p
refix}.part_000{current_part}_of_000{nbr_total_parts}.regions_vs_tracks.scores.
feather or {db_prefix}.part_000{current_part}_of_000{nbr_total_parts}.genes_vs_
tracks.scores.feather).
-g EXTRACT_GENE_ID_FROM_REGION_ID_REGEX_REPLACE, --genes EXTRACT_GENE_ID_FROM_REGION_ID_REGEX_REPLACE
Take top score for a gene by taking the maximum score of multiple regions for
that gene. Define a regex which will remove the non-gene part of the region ID,
so only the gene ID remains. Examples: "gene_id#some_number": "#[0-9]+$" or
"region_id@@gene_id": "^.+@@".
-s SEED, --seed SEED Random seed used for breaking ties when creating rankings for a range of tied
scores. When setting this seed to a specific value and running this script with
the same input, will result in the same rankings databases as output.
-r SSH_COMMAND, --ssh SSH_COMMAND
If defined, run bigWigAverageOverBed over ssh by running the provided command
to make the connection before running bigWigAverageOverBed itself. Example:
'ssh -o ControlMaster=auto -o ControlPath=/tmp/ssh-control-path-%l-%h-%p-%r -o
ControlPersist=600 <hostname>'
```
#### combine_partial_motifs_or_tracks_vs_regions_or_genes_scores_cistarget_dbs.py
```bash
Expand Down Expand Up @@ -382,9 +437,13 @@ Create cisTarget motif databases:
```bash
# FASTA file with sequences per region IDs / gene IDs.
fasta_filename=
# Directory with motifs in Cluster-Buster format.
motifs_dir=
# File with motif IDs (base name of motif file in ${motifs_dir}).
motifs_list_filename=
# cisTarget motif database output prefix.
db_prefix=
nbr_threads=22
Expand All @@ -399,6 +458,47 @@ nbr_threads=22
```
### Score all tracks at once and create rankings
Create cisTarget tracks databases:
- [`create_cistarget_track_databases.py`](#create_cistarget_track_databasespy)
- for each track score all regulatory regions and create a cisTarget tracks vs regions/genes scores db:
- `*.tracks_vs_regions.scores.feather`
- `*.tracks_vs_genes.scores.feather`
- transpose cisTarget track vs regions/genes scores db to cisTarget regions/genes vs tracks scores db:
- `*.regions_vs_tracks.scores.feather`
- `*.genes_vs_tracks.scores.feather`
- creating a ranking for each regulatory region per motif based on the track score of the track for that region
and create a cisTarget track vs regions/genes rankings db:
- `*.tracks_vs_regions.rankings.feather`
- `*.tracks_vs_genes.rankings.feather`
- transpose cisTarget tracks vs regions/genes rankings db to cisTarget regions/genes vs tracks rankings db:
- `*.regions_vs_tracks.rankings.feather`
- `*.genes_vs_tracks.rankings.feather`
```bash
# BED file with regions to score.
regions_bed_filename=
# Directory with bigWig tracks of TF-ChIP-seq data.
tracks_dir=
# File with track IDs (base names of bigWig files in ${tracks_dir}).
tracks_list_filename=
# cisTarget track database output prefix.
db_prefix=
nbr_threads=22
"${create_cistarget_databases_dir}/create_cistarget_motif_databases.py" \
-b "${regions_bed_filename}" \
-T "${tracks_dir}" \
-d "${tracks_list_filename}" \
-o "${db_prefix}" \
-t "${nbr_threads}"
```
### Score motifs in different parts and generate rankings in a separate step
Expand Down Expand Up @@ -445,9 +545,13 @@ This will only create a partial cisTarget motifs vs regions/genes scores databas
```bash
# FASTA file with sequences per region IDs / gene IDs.
fasta_filename=
# Directory with motifs in Cluster-Buster format.
motifs_dir=
# File with motif IDs (base name of motif file in ${motifs_dir}).
motifs_list_filename=
# cisTarget motif database output prefix.
db_prefix=
nbr_threads=22
Expand Down Expand Up @@ -478,10 +582,15 @@ generated cisTarget database as some regions might get lost after liftover. cisT
generated for each species of interest.
```bash
# FASTA file with sequences per region IDs / gene IDs.
fasta_filename=
# FASTA file with sequences per region IDs / gene IDs of the original species.
original_species_fasta_filename=
# Directory with motifs in Cluster-Buster format.
motifs_dir=
# File with motif IDs (base name of motif file in ${motifs_dir}).
motifs_list_filename=
# cisTarget motif database output prefix.
db_prefix=
nbr_threads=22
Expand Down

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