SOLiD BioScope Software protocols

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description
SOLiD BioScope Software computational protocol

SOLiD BioScope Software specifications

Information


Unique identifier OMICS_19505
Name SOLiD BioScope Software
Alternative name BioScope
Software type Pipeline/Workflow
Interface Graphical user interface
Restrictions to use License purchase required
Biological technology Life Technologies
Operating system Unix/Linux, Mac OS, Windows
Computer skills Medium
Stability Stable
Maintained No

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SOLiD BioScope Software IN pipelines

 (12)
2017
PMCID: 5319761
PMID: 28222152
DOI: 10.1371/journal.pone.0171988

[…] barcode trimming, we assessed the quality of the sequencing data using fastqc software. the data were mapped to the reference comprising 980 repeat sequences presented in the mus musculus genome. bioscope software version 1.3 was used for mapping. read counts per repeat family were normalized by library size and then log-transformed. to estimate tumour-associated gene coverage, the data […]

2017
PMCID: 5319761
PMID: 28222152
DOI: 10.1371/journal.pone.0171988

[…] read counts per repeat family were normalized by library size and then log-transformed. to estimate tumour-associated gene coverage, the data was mapped to the mus musculus genome (mm9) with bioscope 1.3. the number of reads mapped to the exons of hmga2, fos, myc and jun was standardized to the library size as rpm (number of reads per million reads in library)., the alteration in exdna […]

2017
PMCID: 5441048
PMID: 28532469
DOI: 10.1186/s40246-017-0107-5

[…] [45], and fastqc software (babraham bioinformatics), and shorter reads (<25) as well as all duplicate reads were deleted. the reads were aligned with the reference genome (grch37 hg19) with bioscope™ (applied biosystems, foster city, ca, usa) using the default settings. results from bioscope™ were filtered by depth >30 reads [46] and quality of the assigned genotype ≥100. […]

2017
PMCID: 5441048
PMID: 28532469
DOI: 10.1186/s40246-017-0107-5

[…] as all duplicate reads were deleted. the reads were aligned with the reference genome (grch37 hg19) with bioscope™ (applied biosystems, foster city, ca, usa) using the default settings. results from bioscope™ were filtered by depth >30 reads [46] and quality of the assigned genotype ≥100. this analysis identified snvs, copy number variants, and frameshift variants (insertion and deletions). […]

2014
PMCID: 3890534
PMID: 24405787
DOI: 10.1186/1471-2164-15-14

[…] [14]., the cdna samples were sequenced using the solid™ 3 plus platform, which allowed the analysis of the gene expression profile of the microorganism in the early exponential phase. using the bioscope programme, unique readings were mapped on the genome, and gene expression was quantified based on the rpkm (reads per kilobase of coding sequence per million mapped) [15]. ribosomal […]

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