The tsRFinder is a lightweight, fast and reliable tool for prediction and annotation of tRNA-derived small RNAs using next-generation sequencing data.
The tsRFinder depends on:
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Perl, v5.10.1 or higher.
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R, v2.15.2 or higher.
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bowtie, v1.0.0 or higher.
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tRNAscan-SE, v1.3.1 or higher, optional.
You may clone tsRFinder by typing the following in the terminal:
git clone https://github.com/wangqinhu/tsRFinder.git
Alternatively, you may download it from:
https://github.com/wangqinhu/tsRFinder/releases/latest
Finally, please add tsR_dir as an environment variable:
echo export tsR_dir="/the/path/of/tsRFinder" >> $HOME/.bashrc
source ~/.bashrc
If you want to run tsRFinder as a system command, create a soft link for it:
ln -s `pwd`/tsRFinder/tsRFinder.pl /usr/local/bin/
A typical tsRFinder job can be easily finished on a modern MacBook (running OS X) or laptop (running Linux), see the following usage and examples.
tsRFinder usage:
tsRFinder.pl <option>
-c Configuration file
-l Label
-g Reference genomic sequence file
-t Reference tRNA sequence file
-s sRNA sequence file
-a Adaptor sequence
-n Min read length [default 18]
-x Max read length [default 45]
-e Min expression level [default 10]
-u Mature tsRNA level cut-off [default 10]
-f sRNA family threshold [default 72]
-d Method for sRNA normalization [default rptm.r/no]
Can be rptm.r/rpm.r/rtpm.m/rptm.m/no
-w tRNA with/without label [default no/yes]
-o Output compressed tarball [default no/yes]
-i Interactive [default yes/no]
-m Mode, run/debug [default run/debug]
-h Help
-v Version
Examples:
tsRFinder.pl -c demo/tsR.conf
tsRFinder.pl -c demo/tsR.alt.conf
To submit tsRFinder job on a cluster managed with sun grid engine (sge), see demo/tsR.sge.sh
Example:
qsub demo/tsR.sge.sh demo/tsR.conf
A full manual could be found in doc/manual.pdf
