ASprofile pipeline

ASprofile specifications

Information


Unique identifier OMICS_01942
Name ASprofile
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Input data A set of gene annotations
Input format GTF
Operating system Unix/Linux
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Maintained Yes

Subtools


  • collect-fpkm
  • extract-as
  • extract-as-fpkm

Download


Versioning


Add your version

Maintainer


  • person_outline Liliana Florea <>

Publication for ASprofile

ASprofile IN pipelines

 (2)
2017
PMCID: 5513552
PMID: 28715466
DOI: 10.1371/journal.pone.0181399

[…] novel genes from tophat alignment were constructed using cufflinks v2.1.1 reference annotation based transcript (rabt) assembly method. the alternative splicing events were found by the software of asprofile v1.0. this approach increased 1828 transcripts in antennae (s2 table). in total, the sequenced fragments created 21,643 genes, 1,828 of them are novel (s2 table). 12,861 of these genes […]

2017
PMCID: 5547134
PMID: 28785060
DOI: 10.1038/s41598-017-07530-z

[…] cleaned reads were aligned to grcm38/mm10 mouse genome assembly using tophat with at most 2 mismatches. alternative splicing (as) events of samples were extracted and compared using the tool asprofile51., hek293t cells were transfected with the corresponding expression plasmids or sirnas (sigma-aldrich, si-ildr1-1: sasi_hs01_00025907; si-ildr1-2: sasi_hs01_00025910; si-ildr2-1: […]

ASprofile institution(s)
Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA; Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
ASprofile funding source(s)
Supported in part by the NSF award ABI-1159078 and NIH grants R01-HG006677 and R01-HG006102.

ASprofile reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review ASprofile