tsRFun: a comprehensive platform for decoding tsRNA expression, functions and prognosis value by highthroughput small RNA-Seq and CLIP-Seq data

Requirements

Linux system, enough disk space and Ram depending on the size of RNA deep sequencing data. (Tested system: ubuntu 12.04 LTS, ubuntu 16.04 LTS)

install conda

wget https://repo.anaconda.com/miniconda/Miniconda3-py39_4.10.3-Linux-x86_64.sh

bash Miniconda3-py39_4.10.3-Linux-x86_64.sh

source ~/.bashrc

configure the environment with conda

conda env create -f tsRFun.yaml

activate conda environment

conda activate tsRFun

test if everything is installed properly:

perl -v

tsRFinder.pl -h

bowtie

samtools

bedtools

run tsRFinder usage

tsRFinder.pl

The input files are: Options:

-i Input could be: .fastq/.fq or .fasta/.fa file.

-o Output address of annotation results.

-t Number of threads to launch (default = 4).

-x Address of bowtie index tRNA information .

Alignment:

-l The minimal length of the output sequences (default = 15)

-L The maximal length of the output sequences (default = 45)

-M The total number of mismatches in the entire alignment (default = 0)

-p The p-value threshold to determine whether the fragment is tsRNA.

Others: -v Print version information

-h Print this usage message

Example of use:

tsRFinder.pl -i PATH_of_example/fasta -o PATH_of_example/ -x hg38_index/

If you have these errors,please refer to the following:

error1

perl: symbol lookup error: perl5/x86_64-linux-thread-multi//auto/Math/CDF/CDF.so: undefined symbol: Perl_Gthr_key_ptr

Solution1

export PERL5LIB=""

error2

samtools: error while loading shared libraries: libtinfow.so.5: cannot open shared object file: No such file or directory

Solution2

conda install -c conda-forge ncurses

zhlingl/tsRFun-conda