FilTar is a tool to integrate RNA-Seq data to pre-existing miRNA target prediction workflows in order to increase prediction accuracy.
It achieves this by:
- Removing transcripts which are not expressed or poorly expressed for a given cell type or tissue
- Generating 3'UTR annotations specific to a given cell type or tissue
It also operates as a fully functional wrapper around the pre-existing TargetScan7 and miRanda target prediction workflows.
Instructions on how to install FilTar can be found at the following location: https://tbradley27.github.io/FilTar/
FilTar can be used by following 2 steps:
- Specify the options you would like to use to run FilTar by editing
config/basic.yaml. - Run the following command:
snakemake --use-conda --cores $N target_predictions.txt
After running the command, all target predictions are contained inside target_predictions.txt.
The following video presents a concise demonstration of basic FilTar usage:
https://www.youtube.com/watch?v=Xhl-nsg7_xo
More detailed instructions can be found inside the full documentation: https://tbradley27.github.io/FilTar/
The article describing FilTar can be found in Volume 36, Issue 8 (pages 2410-2416) of the Bioinformatics journal published by Oxford University Press. An online, open access version of the article is available here.
DOI: 10.1093/bioinformatics/btaa007
PMCID: PMC7178423
PMID: 31930382
The default method of citing the article is to use the following:
Thomas Bradley, Simon Moxon, FilTar: using RNA-Seq data to improve microRNA target prediction accuracy in animals, Bioinformatics, Volume 36, Issue 8, 15 April 2020, Pages 2410–2416, https://doi.org/10.1093/bioinformatics/btaa007
In order to ensure your enquiries are seen by the most people possible who may be sharing your problem, it is best to share the problems that you are having publicly. The first port of call is to post questions on the biostars bioinformatics online forum (https://www.biostars.org/). If using biostars, please make sure to use the 'filtar' tag when asking questions to notify me, so I can answer promptly.
If this option doesn't work for whatever reason, I happen to accept correspondence via my academic email address: thomas.bradley@uea.ac.uk
The issues page of this repository is the best place to post this.
Simox Moxon came up with the original idea and project proposal for FilTar. The FilTar concept was extended and developed further between Simon Moxon and Thomas Bradley through the course of the latter's BBSRC (Biotechnology and Biological Sciences Research Council) PhD Studentship on the Norwich Research Park (NRP) Bioscience Doctoral Training Partnership (DTP) programme, when Thomas Bradley worked under the primary supervision of Simon Moxon initially predominantly at the Earlham Institute, and then later predominantly at the School of Biological Sciences, University of East Anglia.
Full acknowledgements can be found within the preprinted article associated with FilTar.