Data from: Genome-wide discovery and characterization of maize long non-coding RNAs

Li L, Eichten SR, Shimizu R, Petsch K, Yeh C, Wu W, Scanlon MJ, Yu J, Schnable PS, Timmermans MCP, Springer NM, Muehlbauer GJ

Date Published: March 4, 2014

DOI: http://dx.doi.org/10.5061/dryad.4sf33

 

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Content in the Dryad Digital Repository is offered "as is." By downloading files, you agree to the Dryad Terms of Service. To the extent possible under law, the authors have waived all copyright and related or neighboring rights to this data. CC0 (opens a new window) Open Data (opens a new window)

Title LncRNA_Finder - Pipeline Source Code
Downloaded 122 times
Description 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
Download LncRNA_Finder.pl (19.38 Kb)
Download README.txt (2.438 Kb)
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Title all_putative_lncRNAs-Sequence
Downloaded 44 times
Description The transcript sequences of all the 20,163 putative lncRNAs identified in maize
Download all_putative_lncRNAs.fa (11.44 Mb)
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Title all_putative_lncRNAs-GTF
Downloaded 32 times
Description The GTF file of all the 20,163 putative lncRNAs identified in maize
Download all_putative_lncRNAs.gtf (3.149 Mb)
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Title pre-lncRNAs Sequence
Downloaded 36 times
Description The transcript sequences of 18,459 pre-lncRNAs identified in maize
Download pre-lncRNAs.fa (10.58 Mb)
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Title pre-lncRNAs-GTF
Downloaded 35 times
Description The GTF file of 18,459 pre-lncRNAs identified in maize
Download pre-lncRNAs.gtf (2.900 Mb)
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Title High Confidence lncRNAs-Sequence
Downloaded 34 times
Description The transcript sequences of 1,704 High Confidence lncRNAs identified in maize
Download HC-lncRNAs.fa (860.3 Kb)
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Title High Confidence lncRNAs-GTF
Downloaded 37 times
Description The GTF file of 1,704 High Confidence lncRNAs in maize
Download HC-lncRNAs.gtf (248.8 Kb)
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Title Summary of datasets we've used
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Description Transcribed sequences from the maize reference inbred line-B73 were collected from the Sequence Read Archive and GenBank. Data available in the Sequence Read Archive from the maize inbred line B73 included 30 RNA-seq experiments from 13 distinct tissues (leaf, immature ear, immature tassel, seed, endosperm, embryo, embryo sac, anther, ovule, pollen, silk, and root and shoot apical meristem) encompassing a total of 1.168 billion reads with read lengths ranging from 35 to 110 nucleotides. Maize ESTs from a vast variety of tissues and stages were also collected from GenBank and integrated with the maize B73 genome annotation (AGP v2).
Download Datasets_Info.xls (37.88 Kb)
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When using this data, please cite the original publication:

Li L, Eichten SR, Shimizu R, Petsch K, Yeh C, Wu W, Scanlon MJ, Yu J, Schnable PS, Timmermans MCP, Springer NM, Muehlbauer GJ (2014) Genome-wide discovery and characterization of maize long non-coding RNAs. Genome Biology 15(2): R40. http://dx.doi.org/10.1186/gb-2014-15-2-r40

Additionally, please cite the Dryad data package:

Li L, Eichten SR, Shimizu R, Petsch K, Yeh C, Wu W, Scanlon MJ, Yu J, Schnable PS, Timmermans MCP, Springer NM, Muehlbauer GJ (2014) Data from: Genome-wide discovery and characterization of maize long non-coding RNAs. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.4sf33
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