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Protocols

Preseq specifications

Information


Unique identifier OMICS_05451
Name Preseq
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for Preseq

Preseq citations

 (13)
library_books

Purification of nanogram range immunoprecipitated DNA in ChIP seq application

2017
BMC Genomics
PMCID: 5740926
PMID: 29268714
DOI: 10.1186/s12864-017-4371-5

[…] defined error of logarithm of zero. The score of FRiP (fraction of reads in peaks) for each sample was calculated by following the method described in []. The library complexity was calculated by the Preseq package []. […]

call_split

Structural and spatial chromatin features at developmental gene loci in human pluripotent stem cells

2017
Nat Commun
PMCID: 5696376
PMID: 29158493
DOI: 10.1038/s41467-017-01679-x
call_split See protocol

[…] ysis, percentages of the observed cis interactions in the expected total number of cis interactions were calculated for each bait. The total number of distinct cis interactions was estimated by using Preseq software. […]

library_books

Detection of known and novel ALK fusion transcripts in lung cancer patients using next generation sequencing approaches

2017
Sci Rep
PMCID: 5624911
PMID: 28970558
DOI: 10.1038/s41598-017-12679-8

[…] der, CO, USA) according to the manufacturer’s instructions. Briefly, RNA was reverse transcribed using random primers, first strand cDNA was synthesized, and RNA quality was assessed using the Archer PreSeq RNA QC assay (ArcherDX). After second strand cDNA synthesis, end repair and A-tailing steps were performed, cDNA was purified using Agencourt® AMPure® XP beads (Beckman Coulter), and MBC adapte […]

library_books

Comparative performance of the BGISEQ 500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing

2017
GigaScience
PMCID: 5570000
PMID: 28854615
DOI: 10.1093/gigascience/gix049

[…] low you to compute the values for other definitions of endogenous content.The complexity of each library was estimated and extrapolated using the library complexity extrapolation model in the program preseq [], which uses a nonparametric Bayesian Poisson model to estimate the gain in number of unique fragments when the library is sequenced deeper. Instead of using the aligned reads to estimate the […]

library_books

Single cell mRNA isoform diversity in the mouse brain

2017
BMC Genomics
PMCID: 5291953
PMID: 28158971
DOI: 10.1186/s12864-017-3528-6

[…] e : Figure S6 B-C).In order to estimate the true number of isoforms in each single cell, we made use of a recently published Bayesian method to accurately extrapolate the complexity of DNA libraries (Preseq, []). We found that when a cell over time has transcribed 600,000 molecules of mRNA, it will have generated between 5 and 15 conservative isoforms per gene, and between 2 and 4 exon cassette is […]

library_books

Layer specific chromatin accessibility landscapes reveal regulatory networks in adult mouse visual cortex

2017
eLife
PMCID: 5325622
PMID: 28112643
DOI: 10.7554/eLife.21883.061

[…] es (rmdup), index BAM files (index), and calculate library statistics (flagstat). We used CollectInsertSizeMetrics.jar from Picard v1.110 (RRID:SCR_006525) () to analyze fragment size statistics, and preseq v0.1.0 () to analyze library sequencing saturation. The CENTIPEDE package for R () was used to analyze insertions near ATF2 motif locations obtained from the SwissRegulon database (RRID:SCR_005 […]

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Preseq institution(s)
Department of Mathematics and Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA

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