Scripture pipeline

Scripture specifications


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

Publication for Scripture

Scripture IN pipelines

PMCID: 5663602
PMID: 29137430
DOI: 10.18632/oncotarget.21031

[…] reads are shown in supplementary figure 2 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 […]

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 cufflinks50 and scripture51. 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. […]

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) [46]. the mapped reads of each sample were assembled by both scripture (beta2) [47] and cufflinks (v2.1.1) [48] in a reference-based approach., cuffdiff (v2.1.1) was used to calculate fpkms (fragments per kilo-base of exon per million fragments mapped) […]

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 […]

PMCID: 3552696
PMID: 23369519
DOI: 10.1186/1755-8794-6-S1-S7

[…] donor and acceptor sites within the 100,000 bases span. the minimum intronic length is set to be 70 bases. after aligning the remaining unmapped reads to the new lincrna junction library, we used scripture [42] for predicting the lincrna exonic structures with default settings. similar as for mrnas and pre-mirnas, the expression levels of lincrnas were further quantified by the total number […]

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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