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-3pipeline-LncRNA_Finder的源代码 免责声明：本软件由作者及贡献者按"原样"提供，不作出任何明示或暗示的担保，包括但不限于对适销性和特定用途适用性的默示担保。在任何情况下，林莉、内森·M·斯普林格（Nathan M. Springer）、加里·J·米尔鲍尔（Gary J. Muehlbauer）（或明尼苏达大学）均不对任何直接、间接、附带、特殊、惩戒性或继发性损害（包括但不限于采购替代商品或服务；损失使用、数据或利润；或业务中断）承担责任，无论该责任依据合同、严格责任还是侵权（包括过失或其他情形）产生，即便已被告知此类损害发生的可能性。 功能描述：LncRNA_Finder可基于原生序列FASTA格式文件实现长链非编码RNA（long noncoding RNA, lncRNA）的挖掘。本脚本本质上依托外部比对工具的输出结果，通过一系列预设参数完成长链非编码RNA的筛选过滤。 2. 外部软件依赖 需在本地环境中正确安装NCBI BLAST独立安装包、Bowtie与CPC工具，并在流程起始处配置外部程序的运行路径。 3. 使用方法 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>] 可选参数： -i <transcript.fasta> -p <protein.fasta> -k <housekeeping.fasta> -s <smallRNA.fasta> -o <output prefix> -h 显示帮助信息 -t <int> 计算所用线程数 || 默认值：4 -r <int> lncRNA最小长度阈值 || 默认值：200 -f <int> lncRNA最大潜在开放阅读框（Open Reading Frame, ORF）长度阈值 || 默认值：100 -m <int> 与小RNA序列比对时的错配数 || 默认值：0 -e 针对蛋白质数据库的比对E值 || 默认值：1.0×10^-3