To learn more, please see our preprint in BioRxiv: https://www.biorxiv.org/content/10.1101/672931v1
Newer version of TALON (v4.0+) are designed to be run with Python 3.7 (tested specifically with Python 3.7.2). Older versions of TALON use Python 2.7.
To install TALON, simply download the files using Github's "Download ZIP" button, then unzip them in the directory where you would like to store the program. Alternately, you can download a specific version of the program from the Releases tab. The TALON scripts are run directly from the command line- just include the path.
The first step in using TALON is to initialize a SQLite database from the GTF annotation of your choice (i.e. GENCODE). This step is done using initialize_talon_database.py, and only needs to be performed once. Keep track of the build and annotation names you choose, as these will be used downstream when running TALON and its utilities.
python initialize_talon_database.py --h
Usage: initialize_talon_database.py [options]
Options:
-h, --help Show help message and exit
--f GTF annotation file
--g The name of the reference genome build that the annotation describes. Use a short and memorable name since you will need to specify the genome build when you run TALON later.
--a The name of the annotation (for metadata purposes)
--l Minimum required transcript length (default = 300 bp)
--idprefix Prefix for naming novel discoveries in eventual TALON runs (default = 'TALON')
--5p Maximum allowable distance (bp) at the 5' end during annotation (default = 500 bp)
--3p Maximum allowable distance (bp) at the 3' end during annotation (default = 300 bp)
--o Output prefix for the database
Now that you've initilialized your database, you're ready to annotate long read datasets using TALON. The input database is modified in place to track and quantify transcripts in the provided dataset(s). You can add more datasets at any time by creating a config file for them and running this command.
python talon.py --h
Usage: talon.py [options]
Options:
-h, --help Show help message and exit
--f Comma-delimited dataset config file providing sam files for TALON to run on, as well as metadata that will be tracked in the dataset table. The required format is: dataset name, sample description, platform, sam file (full path).
--db FILE, TALON database. Created using build_talon_annotation.py
--build STRING, Genome build (i.e. hg38) to use. Must be in the
database.
--cov, -c Minimum alignment coverage in order to use a SAM entry. Default = 0.9
--identity, -i Minimum alignment identity in order to use a SAM entry. Default = 0
--o OUTPREFIX Prefix for output files
If you have run TALON on biological replicates or other datasets you would like to leverage for quality control, you might want to obtain a filtered list of transcripts that are 1) known, or 2) reproducible in at least two of your datasets. To get such a list, run the following TALON utility:
python post-TALON_tools/filter_talon_transcripts.py --h
Options:
-h, --help show this help message and exit
--db=FILE TALON database
-a ANNOT, --annot=ANNOT
The name of the annotation version to use.
Will determine which annotation transcripts
are considered known or novel relative to.
Note: must be in the TALON database.
-p FILE, --pairings=FILE
Optional: A file indicating which datasets
should be considered together when filtering
novel transcripts (i.e. biological replicates).
Format: Each line of the file constitutes a group,
with member datasets separated by commas.
If no file is provided, then novel transcripts
appearing in any two datasets will be accepted.
--o=FILE Outfile name
The columns in the resulting output file are:
- TALON gene ID (an integer). This is the same type of ID found in column 1 of TALON abundance files.
- TALON transcript ID (an integer). This is the same type of ID found in column 2 of TALON abundance files.
- Novelty category designation of transcript.
If you would like to extract an abundance matrix for your TALON-processed datasets, use the script create_abundance_file_from_database.py from the post-TALON_tools directory.
python post-TALON_tools/create_abundance_file_from_database.py --h
Usage: create_abundance_file_from_database.py [options]
Options:
-h, --help show this help message and exit
--db=FILE TALON database
-a ANNOT, --annot=ANNOT
Which annotation version to use. Will determine which
annotation transcripts are considered known or novel
relative to. Note: must be in the TALON database.
-b BUILD, --build=BUILD
Genome build to use. Note: must be in the TALON
database.
--filter If this option is set, the transcripts in the
database will be filtered prior to GTF creation
(for more information, see
filter_talon_transcripts.py)
-p FILE, --pairings=FILE
Optional (only relevant if filter = true): A file
indicating which datasets should be
considered together when filtering
novel transcripts (i.e. biological replicates).
Format: Each line of the file constitutes a group,
with member datasets separated by
commas. If no file is provided, then
novel transcripts appearing in any
two datasets will be accepted.
--o=FILE Prefix for output file
The columns in the abundance file are as follows:
- TALON gene ID
- TALON transcript ID
- Gene ID from your annotation of choice. If the gene is novel relative to that annotation, this will be 'NA'.
- Transcript ID from your annotation of choice. If the transcript is novel relative to that annotation, this will be 'NA'.
- Gene name from your annotation of choice (makes the file a bit more human-readable!). If the transcript is novel relative to that annotation, this will be the TALON-derived name.
- Transcript name from your annotation of choice. If the transcript is novel relative to that annotation, this will be the TALON-derived name.
- Number of exons in the transcript
- Length of transcript model (basepairs)
- Gene novelty (Known, Antisense, Intergenic)
- Transcript status (Known, ISM, NIC, NNC, Antisense, Intergenic)
- ISM subtype (Both, Prefix, Suffix, None)
---------------------------- Remaining columns -----------------------------
One column per dataset, with a count indicating how many times the current transcript was observed in that dataset.
python post-TALON_tools/create_GTF_from_database.py --h
Options:
-h, --help show this help message and exit
--db=FILE TALON database
-b BUILD, --build=BUILD
Genome build to use. Note: must be in the TALON
database.
-a ANNOT, --annot=ANNOT
Which annotation version to use. Will determine which
annotation transcripts are considered known or novel
relative to. Note: must be in the TALON database.
--whitelist=FILE Whitelist file of transcripts to include in the
output. First column should be TALON gene ID,
second column should be TALON transcript ID.
Other columns are ignored.
--observed If this option is set, the GTF file will only
include transcripts that were observed in at least one
dataset (redundant if dataset file provided).
-d FILE, --datasets=FILE
Optional: A file indicating which datasets should be
included (one dataset name per line). Default is to
include all datasets.
--o=FILE Prefix for output GTF
MIT, see LICENSE
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