LncRNA_Finder - Pipeline Source Code

Source code of the pipeline-LncRNA_Finder

THIS SOFTWARE IS PROVIDED BY THE AUTHORS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL LIN LI, NATHAN M. SPRINGER, or GARY J. MUEHLBAUER (OR UNIVERSITY OF MINNESOTA) BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

DESCRIPTION: LncRNA_Finder enables the discovery of long noncoding RNAs using native sequence fasta files. This script essentially uses the results from external alignment programs and performs long noncoding RNA filtering via a set of specified parameters.
2, Prerequisite of external softwares
Need to install ncbi_blast standalone package, bowtie and cpc in your local environment correctly and set the running path of external programs at the beginning of the pipeline

3, Usage
Perl LncRNA_Finder.pl -i <transcript.fasta> -p <protein.fasta> -k <housekeeping.fasta> -s <smallRNA.fasta> -o <output prefix> [-t <# of thread>] [-r <minimum lncRNA length>] [-f <maximum ORF length>] [-m <# of mismatch>] [-e <E-value of alignment>]

Options:

-i <transcript.fasta>

-p <protein.fasta>

-k <housekeeping.fasta>

-s <smallRNA.fasta>

-o <output prefix>

-h help

-t <int> number of thread for the computation || default=4

-r <int> minimum lncRNA length || default=200

-f <int> maximum potential ORF length of lncRNAs || default=100

-m <int> number of mismatch in the alignment with smallRNA || default=0

-e E-value of the alignment against protein database || default=1.0e-3