OLego protocols

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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 olego 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 software 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 […]


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OLego in publications

 (12)
PMCID: 5821855
PMID: 29467410
DOI: 10.1038/s41467-018-02891-z

[…] sequencing was performed on the nextseq on a 1 × 75 high output flow cell following the nextseq denature and dilute guide (protocol a: standard normalization method)., rnaseq data was mapped with olego version 1.1.5 and normalized by using tpm (transcripts per millions) analysis as shown in supplementary figure . total number of reads mapped to a known transcript annotation was estimated […]

PMCID: 5485934
PMID: 28545234
DOI: 10.3390/ijms18061110

[…] number of supporting alignments []filter out alignments assessed as low confidence by regression model (basing on nucleotide distributions around splice junctions and intron size, as implemented in olego) []., restrict alignment gaps to a small subset of possible intronic dinucleotides (as implemented in tophat), filter on alignment gaps supported by minimal 20 matching nucleotides on each side […]

PMCID: 5397481
PMID: 28473753
DOI: 10.3389/fncel.2017.00093

[…] illumina hiseq 2000 sequencer. sequencing data were processed using bioinformatics pipeline provided by the mit biomicrocenter. briefly, illumina reads were mapped onto the rat genome (rn5) using olego software (wu et al., ), differential gene expression analysis was obtained with deseq (anders and huber, ), and spotfire (tibco) was used for gene clustering. gene mapping on signaling pathways […]

PMCID: 5300003
PMID: 27869056
DOI: 10.1017/S003118201600189X

[…] to assess its functions. up to now, there is no knockout available. however, in t. brucei, the rnai of three calpain genes revealed their roles in parasite growth, morphology and flagellum assembly (olego-fernandez et al. ; hayes et al. )., there are several other evidences on the relevance of calpain molecules for leishmania life cycle disclosed by unbiased assays, such as transcriptomics […]

PMCID: 5140759
PMID: 27775709
DOI: 10.1038/nsmb.3310

[…] the equivalent of 50 ng of oligo(dt)-primed cdna (reverse transcription performed with superscript iii, life technologies) and 35 cycles of pcr amplification. for as analysis of rna-seq data we used olego and quantas software suite as previously described . tandem utr isoform analysis was performed with the miso algorithm v0.5.2 using default settings , except for use of custom 3′utr isoform […]


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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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