===============================================================================
       tRFanalyzer, a tool for quantifying tRNAs and tRNA-derived 
                        fragments (tRFs) in plants.
===============================================================================

    Version 1.0


    This program is free software: you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation, either version 3 of the License, or    
    (at your option) any later version.

    This program is distributed in the hope that it will be useful,      
    but WITHOUT ANY WARRANTY; without even the implied warranty of       
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the       
    GNU General Public License for more details.

    
    Contact: skyxma@tjnu.edu.cn


===============================================================================
                                  Description
===============================================================================

tRFanalyzer consists of two sections. In section I, after removal of rRNA 
reads, tiny (10~16-nt) and short (17~40-nt) sRNA reads are mapped to 
tRNA-masked genome, and the unmapped reads are further mapped to mature tRNAs.
The fractional weighting algorithm (Johnson et al. G3, 2016) is adopted to 
alocate multi-mapping tRNA reads, and subsequently the abundances of tRFs are 
measured.

The section II of tRFanalyzer deals with tRNA-seq long reads (>40-nt) for 
quantification of mature tRNA levels. The rRNA reads are first removed, 
then, any 'CCA' at the 3' terminus of long reads is trimmed. The trimmed 
reads are mapped to genome, followed by retrieving the reads overlapped 
with the precursor tRNA loci. Fractional weighting algorithm is used to 
allocate multi-mapping reads, and finally, the expressions of mature tRNAs 
are quantified.





===============================================================================
                                 Prerequisites
===============================================================================

OS Platform: Linux
Perl 5.10, or above

Executables under PATH:
bowtie          (http://bowtie-bio.sourceforge.net/index.shtml)
bowtie2         (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml)
hisat2          (https://ccb.jhu.edu/software/hisat2/index.shtml)
samtools        (http://samtools.sourceforge.net/)
intersectBed    (https://bedtools.readthedocs.io/en/latest/)





===============================================================================
                                 Tests
===============================================================================

Download tRFanalyzer, uncompress it, and then cd to the test folder.

1. Run the following command to analyze Arabidopsis paired-end tRNA-seq data.

   perl tRFanalyzer.pl -d PEdat/ -o out1 -s ath


2. Run the following command to analyze rice single-end sRNA-seq data.

   perl tRFanalyzer.pl -d SEdat/ -o out2 -s osa -t 2





===============================================================================
                                 Notes
===============================================================================

1. The executables bowtie, bowtie2, hisat2, samtools, intersectBed 
   should be under PATH.

2. Paired-end tRNA-seq data file extensions should be _R1.fq and _R2.fq.
   Single-end data file extensions should be _R1.fq.