L1 Chimeric Transcripts (LCTs) are transcribed from LINE 1 antisense promoter and include the L1 5’UTR sequence in antisense orientation followed by the adjacent genomic region. CLIFinder v0.5.2 is a Galaxy tool, specifically designed to identify potential LCTs from one or several oriented RNA-seq paired-end reads in the human genome. CLIFinder v0.5.2 is customizable to detect transcripts initiated by different types of repeat elements.
Some tools are used by CLIFinder that must be installed and added to the PATH (listed in CLIFinder.xml). This is easily done through conda with the command:
conda create -n clifinder samtools=1.9 bedtools=2.26.0gx repeatmasker=4.0.9_p2 bwa=0.7.17 fastx_toolkit=0.0.14 perl=5.26.2 perl-getopt-long=2.50 perl-file-copy-recursive=0.45 perl-parallel-forkmanager=2.02 perl-statistics-r=0.34 r-base=3.5.1 r-plyr=1.8.5 bioconductor-genomicranges=1.34.0 wget=1.20.1
You should then be able to use CLIFinder by activating the conda environment and running the script with:
conda activate clifinder perl script/CLIFinder.pl
Galaxy uses conda to solve tool requirements starting with Galaxy release 16.01 so that is the minimum version required to install this tool (which can be done through the toolshed: https://toolshed.g2.bx.psu.edu/repository?repository_id=5c73d1cf20ab37c3).
The command you need to use to run the script is as follows:
CLIFinder.pl --first <first fastq of paired-end set 1> --name <name 1> --second <second fastq of paired-end set 1> [--first <first fastq of paired-end set 2> --name <name 2> --second <second fastq of paired-end set 2> ...] --ref <reference genome> [--build_ref] --TE <transposable elements> [--build_TE] --html <results.html> --html-path <results directory> [options]
Arguments:
--first <fastq file> First fastq file to process from paired-end set
--name <name> Name of the content to process
--second <fastq file> Second fastq file to process from paired-end set
--ref <reference> Fasta file containing the reference genome
--TE <TE> Fasta file containing the transposable elements
--rmsk <text file> Tab-delimited text file (with headers) containing reference repeat sequences (e.g. rmsk track from UCSC)
--refseq <text file> Tab-delimited file (with headers) containing reference genes (e.g. RefGene.txt from UCSC)
--html Main HTML file where results will be displayed
--html-path Folder where results will be stored
For any fasta file, if a bwa index is not provided, you should build it through the corresponding '--build_[element]' argument
Options:
--rnadb <RNA db> Blast database containing RNA sequences (default: empty)
--estdb <EST db> Blast database containing EST sequences (default: empty)
--size_read <INT> Size of reads (default: 100)
--BDir <0|1|2> Orientation of reads (0: undirectional libraries, 1: TEs sequences in first read in pair, 2: TEs sequences in second read in pair) (default: 0)
--size_insert <INT> Maximum size of insert tolerated between R1 and R2 for alignment on the reference genome (default: 250)
--min_L1 <INT> Minimum number of bp matching for L1 mapping (default: 50)
--mis_L1 <INT> Maximum number of mismatches tolerated for L1 mapping (default: 1)
--min_unique <INT> Minimum number of consecutive bp not annotated by RepeatMasker (default: 33)
--species <STRING> Species to use in RepeatMasker (default: human)
--threads <INT> Number of threads (default: 1)
For Blast database files, if a fasta is provided, the database can be built with '--build_[db]'. Otherwise, provide a path or URL. "tar(.gz)" files are acceptable, as well as wild card (rna*) URLs.