OLego pipeline

OLego specifications

Information


Unique identifier OMICS_01244
Name OLego
Software type Application/Script
Interface Command line interface
Restrictions to use None
Biological technology Illumina
Operating system Unix/Linux, Mac OS
Programming languages C++
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.1.7
Stability Stable
Maintained Yes

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Maintainers


  • person_outline Chaolin Zhang <>
  • person_outline Michael Zhang <>
  • person_outline Jie Wu <>

Additional information


https://zhanglab.c2b2.columbia.edu/index.php/OLego_Documentation

Publication for OLego

OLego IN pipelines

 (2)
2018
PMCID: 5840295
PMID: 29511296
DOI: 10.1038/s41598-018-21371-4

[…] research. illumina rna-seq reads were de-multiplexed based on sample-specific barcodes using fastq-tools yielding ~30 million reads per sample. reads were mapped to the human genome (hg19) using olego38 and bedgraph files were generated using bedtools to facilitate visualization of read coverage on the ucsc genome browser. quantification of reads associated with annotated genomic features […]

2015
PMCID: 4830686
PMID: 26192745
DOI: 10.1038/nn.4065

[…] studies reveal marked differences in gene expression patterns between c9als and sals, with substantially more changes observed in c9als, especially in the cerebellum., to evaluate as changes in als, olego software30 was used to align rnaseq reads to the hg19 genome assembly and splice junctions. the total number of as events [false discovery rate (fdr) < 0.05] was over 3 times higher in c9als […]

OLego institution(s)
Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA; Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA; Department of Molecular and Cell Biology, Center for Systems Biology, The University of Texas at Dallas, Richardson, TX, USA; Bioinformatics Division, Center for Synthetic and Systems Biology, TNLIST, Tsinghua University, Beijing, China; Laboratory of Molecular Neuro-Oncology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
OLego funding source(s)
Supported by National Institutes of Health (NIH) [GM74688, K99GM95713] and National Basic Research Program of China [2012CB316503].

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