Protocols

SCRIPT-MAP specifications

Information


Unique identifier OMICS_28261
Name SCRIPT-MAP
Alternative name Spectrometry response CuRve of entIre Peptide-Transition ions in MAmmalian Proteome
Restrictions to use None
Database management system MySQL
Community driven No
Data access Browse
User data submission Not allowed
Maintained Yes

Maintainers


  • person_outline Jun Qin
  • person_outline Chen Ding

Information


Unique identifier OMICS_28261
Name SCRIPT-MAP
Alternative name Spectrometry response CuRve of entIre Peptide-Transition ions in MAmmalian Proteome

Maintainers


This tool is not maintained anymore.

Publication for Spectrometry response CuRve of entIre Peptide-Transition ions in MAmmalian Proteome

SCRIPT-MAP citations

 (2)
library_books

Metagenomic binning of a marine sponge microbiome reveals unity in defense but metabolic specialization

2017
PMCID: 5649159
PMID: 28696422
DOI: 10.1038/ismej.2017.101

[…] the sub-contigs with bowtie2 v. 2.2.2 at default settings (). The resulting SAM files were converted to BAM, sorted and indexed with samtools v. 0.1.18 (), and duplicates were marked according to the script map-bowtie2-markduplicates.sh provided with the CONCOCT package (). Samtools v. 0.1.18 was also used for depth calculation (). The in-house python script avgcov_from_samtoolsout.py (https://git […]

call_split

Potential for hydrogen oxidizing chemolithoautotrophic and diazotrophic populations to initiate biofilm formation in oligotrophic, deep terrestrial subsurface waters

2017
Microbiome
PMCID: 5364579
PMID: 28335808
DOI: 10.1186/s40168-017-0253-y
call_split See protocol

[…] edicted and annotated by Prokka was calculated using bedtools v2.17.0 [] and the scripts prokkagff2bed.sh and get_coverage_for_genes.py, after the raw reads were mapped back to the assembly using the script map-bowtie2-markduplicates.sh. These scripts, developed by the Environmental Genomics group at SciLifeLab Stockholm, are available at http://metagenomics-workshop.readthedocs.io/. Gene coverage […]

SCRIPT-MAP institution(s)
State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing, China; National Center for Protein Sciences (The PHOENIX Center), Beijing, China; Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA; State Key Laboratory of Genetic Engineering, Human Phenome Institute, Institutes of Biomedical Sciences, Shanghai, China; School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
SCRIPT-MAP funding source(s)
Supported by International Science & Technology Cooperation Program of China (2014DFB30010; 2014DFA33160; 2012DFB30080), National Program on Key Basic Research Project (973 Program, 2014CBA02000; 2012CB910300), National Key Research and Development Program of China (2017YFC1308900, 2017YFA0505102 and 2017YFC0908404), National High-tech R&D Program of China (863 program, 2012AA020201), National Natural Science Foundation of China (31200582; 31170779; 31200992; 31270822; 31770886 and 31700682), Beijing Natural Science Foundation (5132012; Z131100005213003) and Shanghai Municipal Science and Technology Major Project (2017SHZDZX01).

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