Scripture protocols

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Scripture specifications

Information


Unique identifier OMICS_01265
Name Scripture
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainers


  • person_outline Mitchell Guttman <>
  • person_outline Manuel Garber <>
  • person_outline Aviv Regev <>

Publication for Scripture

Scripture in pipelines

 (10)
2017
PMCID: 5663602
PMID: 29137430
DOI: 10.18632/oncotarget.21031

[…] of the above mapped reads are shown in and are based on genomic overlap with existing annotations using the htseq programme. a total of 274,470 assembled transcripts were produced using both scripture (beta2) and cufflinks (v2.1.1). after basic filtering and coding potential filtering, a total of 7,764 putative lncrna transcripts were identified, including 6,179 transcript isoforms […]

2016
PMCID: 4707302
PMID: 26793234
DOI: 10.3389/fgene.2015.00361

[…] are traversed in the graph to find transcript variants (martin and wang, ). two transcriptome assemblers that are commonly used for graph building and traversal are cufflinks (trapnell et al., ) and scripture (guttman et al., ). the computational requirements of reference-based transcriptome assembly are significantly less compared to de novo transcriptome assembly. furthermore, the presence […]

2016
PMCID: 4877582
PMID: 27216292
DOI: 10.1038/srep26604

[…] individual libraries were converted to the fastq format. sequence reads were aligned to the human genome (hg19) with tophat2 and the resulting alignment files were reconstructed with cufflinks and scripture. for mrna analyses, the refseq database (build 37.3) was chosen as the annotation references. for lncrna analyses, the gencode v19 database was chosen as the annotation references. […]

2016
PMCID: 5053085
PMID: 27716141
DOI: 10.1186/s12864-016-3122-3

[…] reads were generated. demultiplexed and quality filtered reads were then aligned to rat reference assembly (rn5) using tophat (v.2.0.9) []. the mapped reads of each sample were assembled by both scripture (beta2) [] and cufflinks (v2.1.1) [] in a reference-based approach., cuffdiff (v2.1.1) was used to calculate fpkms (fragments per kilo-base of exon per million fragments mapped) of coding […]

2015
PMCID: 4511015
PMID: 26201343
DOI: 10.1186/s13059-015-0702-5

[…] in which reads appear in the alignment file that is used as input to an isoform quantification method is ‘randomized’ whenever the quantification method recommends sorting alignments by read name., scripture and cem require annotation files in a bed-based format which supports multiple fragments (that is, exons) per entry and is known as bed12 or bed12+3. these were generated […]


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Scripture in publications

 (51)
PMCID: 5946474
PMID: 29747577
DOI: 10.1186/s12864-018-4754-2

[…] count ≥2) and their differences from other classes of rnas (eg. mrnas, rrnas, trnas, snrnas, snornas, pre-mirnas, and pseudogenes), the transcripts were classified into different subtypes using both scripture beta2 and cufflinks (v2.1.1). 93.98% of the identified transcripts (50,857) were known as the reference transcripts, whereas 6.02% (3061) were the presumed lncrnas. to further confirm […]

PMCID: 5879571
PMID: 29609543
DOI: 10.1186/s12863-018-0608-9

[…] of the goat and rat genomes respectively. index of the reference genome was created by bowtie v2.0.6 [, ] and then we aligned paired-end clean reads to the reference genome using tophat v2.0.9 []. scripture (beta2) [] and cufflinks (v2.1.1) [, ] were adopted to assemble the reads of each sample in a reference-based approach. both methods determined exons connectivity by spliced reads. […]

PMCID: 5923456
PMID: 29601508
DOI: 10.3390/v10040162

[…] of the reference genome was built using bowtie v2.0.6 and paired-end clean reads were aligned to the reference genome using tophat v2.0.9. the mapped reads from each sample were assembled using both scripture (beta2) and cufflinks (v2.1.1) [,]. the distributions of reads for known genes were analyzed using htseq []., four coding potential analysis software packages, cnci, phylocsf with default […]

PMCID: 5876304
PMID: 29628875
DOI: 10.3389/fnmol.2018.00091

[…] was built using bowtie v2.0.6 and the paired-end clean reads were aligned with the reference genome using tophat v2.0.9 (trapnell et al., )., the mapped reads of each sample were assembled by both scripture (beta2) (guttman et al., ) and cufflinks (v2.1.1) (trapnell et al., ), following the reference. both methods use spliced reads to determine the exon connectivity, via different approaches. […]

PMCID: 5862966
PMID: 29563515
DOI: 10.1038/s41598-018-23334-1

[…] b. oleracea and b. rapa,, were built using bowtie v2.0.6 (broad institute, cambridge, ma, usa). sequencing reads were aligned to the reference genome using tophat v2.0.9, and assembled by both scripture (beta2) and cufflinks (v2.1.1)., we selected transcripts which met the following criteria: length ≥ 200 bp; read coverage > 3; presence in both sample replicates and both assemblies […]


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Scripture institution(s)
Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA; Department of Systems Biology, Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
Scripture funding source(s)
Supported by a Burroughs Wellcome Fund Career Award at the Scientific Interface, an NIH PIONEER award, an NHGRI R01, and the Howard Hughes Medical Institute, and NHGRI and the Broad Institute of MIT and Harvard.

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