ngs.plot protocols

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ngs.plot specifications

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Unique identifier OMICS_00922
Name ngs.plot
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python, R
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Requirements
doMC, BSgenome, Rsamtools, ShortRead
Maintained Yes

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  • person_outline Li Shen <>
  • person_outline Lisa Placanica <>

Publication for ngs.plot

ngs.plot in pipelines

 (9)
2018
PMCID: 5787291
PMID: 29373953
DOI: 10.1186/s12864-017-4397-8

[…] –pi) []. an fdr of 0.05 was used for dynamic nucleosome calling, except for position shift where a range setting of 50–95 bp was used. genome-wide nucleosome patterns were plotted using danpos [] or ngs.plot []. nucleosome occupancy were determined as averaged reads per million mapped reads. igv was used to visualize mapped reads to the reference genome []. the genome annotation was obtained […]

2017
PMCID: 5206674
PMID: 28045116
DOI: 10.1038/srep39883

[…] genome assembly 10.2 with bowtie2 (version 2.1.0) with default parameters. the picard toolkit was applied to remove pcr duplicates (version 1.118; http://broadinstitute.github.io/picard/). the ngs.plot program was used to visualize the read coverage of medip around each gene body and tss region. medip quality assessment and dna methylation score (reads per kilobases per million reads […]

2017
PMCID: 5469463
PMID: 28609438
DOI: 10.1371/journal.pone.0178363

[…] inspection of individual loci. the bed files were also used for calculating and visualizing the relative enrichment levels of h4k16ac within the genic region of the mouse gene catalogue with the ngs.plot program []. the raw sequences and processed data have been deposited to the geo database (gse97459). the gene network analyses were performed with the gorilla program using a subset […]

2017
PMCID: 5919733
PMID: 29223978
DOI: 10.1534/g3.117.300311

[…] using macs 1.4 at default settings. association of peaks with specific genes was performed using pavis (). specific h3k27me3 peaks were visualized using the integrated genome viewer (igv) (; ). ngs.plot was used to generate the average fold enrichment of h3k27me3 overview across the gene bodies ()., the cm+ectoderm was manually isolated and dissociated by incubating the tissue in 0.25% […]

2016
PMCID: 4978704
PMID: 27475226
DOI: 10.1016/j.celrep.2016.06.096

[…] a region 100 nt up- and downstream of the peak. the 5mer is centered at the reported positions., the distribution of ejcs over the whole length of different mrnas and exons was calculated using the ngs.plot software () with ensembl 75 annotation. to visualize the differences between rna-seq and ejc iclip signals, the exons were ranked with the parameter “-go diff”., we searched for ejc binding […]


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ngs.plot in publications

 (58)
PMCID: 5958073
PMID: 29773913
DOI: 10.1038/s41598-018-25963-y

[…] ‘-nomodel -nolambda -keep-dup all -call-summits -q 0.01’. output bedgraph format files were used to visualize accessible regions. the distribution of accessible chromatin was analyzed using ngs.plot. two biological replicates were analyzed and similar results were obtained. the sequencing data are deposited at ddbj (accession number dra006829)., nuclei were isolated as described below. […]

PMCID: 5946721
PMID: 29719263
DOI: 10.1016/j.celrep.2018.04.004

[…] the cross-induced mutation sites (cims) pipeline and reads per transcript counted with htseq (, ). genome coverage was calculated using bedtools, and the read distribution profile was plotted with ngs.plot, with combined data for all replicates (, ). input sequencing, alignment, and quantification are described in the section. rpkm and cpm values were obtained from the edger package (). […]

PMCID: 5923290
PMID: 29703894
DOI: 10.1038/s41467-018-04132-9

[…] h3k9me3 on ervs between imefs and escs, we performed a chip-qpcr analysis of h3k9me3 on selected ervs and major satellite repeats for both cell types (fig. ). consistent with previous results and ngs plot data (fig. ), h3k9me3 was enriched in the repeat domains of wt escs, but exhibited much less enrichment on such repeats in imefs. after setdb1 depletion in setdb1 cko mescs and imefs, […]

PMCID: 5844884
PMID: 29523784
DOI: 10.1038/s41467-018-03264-2

[…] available databases and indicated papers. venn diagrams were generated using the online tool. tag density plots around the center of enhancers regions were quantified with the ngsplot 2.47 command ngs.plot.r and plotted with graphpad prism (graphpad software, san diego, california, usa, www.graphpad.com). normalized bigwig tracks of chip-seq experiments were generated with bedtools 2.24.0 […]

PMCID: 5948225
PMID: 29766023
DOI: 10.1016/j.omtm.2018.02.002

[…] structures of selected reads were visualized by mfold. constraints to force base-pairing of itr regions were used. other parameters were set to default. aggregation plots were generated using ngs.plot (version 2.41)., to distinguish reads associated with the λdna spike-in versus the vector genome dna pool, reads were simply mapped to either the λ-phage genome or the respective vector […]


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ngs.plot institution(s)
Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
ngs.plot funding source(s)
Supported by the Friedman Brain Institute and the National Institutes of Health [P50MH096890 and P01DA008227].

ngs.plot review

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Fabien Pichon

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Desktop
I use it to generate heatmaps and average profiles. Works good. You can choose to center your plots on TSS or on genebody and even enhancers (but works worse because of the incomplete database, of course). Usefull to quickly see if your reads or peaks are located where you expect them or not.