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Rsamtools specifications

Information


Unique identifier OMICS_29383
Name Rsamtools
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format BAM,FASTA,BCF
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Artistic License version 2.0
Computer skills Advanced
Version 1.32.3
Stability Stable
Requirements
methods, KEGG.db, utils, BiocStyle, GenomicAlignments, zlibbioc, BiocParallel, BSgenome.Hsapiens.UCSC.hg19, RUnit, GenomicFeatures, S4Vectors(>=0.17.25), IRanges(>=2.13.12), Biostrings(>=2.47.6), GenomicRanges(>=1.31.8), TxDb.Dmelanogaster.UCSC.dm3.ensGene, RNAseqData.HNRNPC.bam.chr14, GenomeInfoDb(>=1.1.3), XVector(>=0.19.7), BiocGenerics(>=0.25.1), bitops, TxDb.Hsapiens.UCSC.hg18.knownGene, ShortRead(>=1.19.10)
Maintained Yes

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Versioning


No version available

Documentation


Additional information


http://bioconductor.org/packages/release/bioc/vignettes/Rsamtools/inst/doc/Rsamtools-Overview.pdf

Rsamtools citations

 (71)
library_books

B cell activation and plasma cell differentiation are inhibited by de novo DNA methylation

2018
Nat Commun
PMCID: 5953949
PMID: 29765016
DOI: 10.1038/s41467-018-04234-4

[…] ng Bismark (v0.16.3) using the following options: “--bam --chunkmbs 1024 –multicore 8”. Mapped BAM files were sorted with SAMtools (v0.1.19-96b5f2294a) and methylation calls were extracted using the “Rsamtools” (v.1.22.0) and “data.table” (v.1.9.6) packages, as well as custom R scripts as previously described. Coverage was determined for all CpGs with 10× coverage in each sample (N = 615,148) and […]

library_books

Early life diet conditions the molecular response to post weaning protein restriction in the mouse

2018
BMC Biol
PMCID: 5930764
PMID: 29720174
DOI: 10.1186/s12915-018-0516-5

[…] us rDNA reference, using Bowtie2 (v2.1.0). Only reads that mapped to the correct starting position and perfectly matched the consensus were used for further analysis. For rDNA analysis, the R package RSamtools was used to identify each read as either having an A or a C at position −104 bp and to determine the methylation status at position −133 bp of each read. Reads could therefore be assigned to […]

library_books

An intronic VNTR affects splicing of ABCA7 and increases risk of Alzheimer’s disease

2018
Acta Neuropathol
PMCID: 5954066
PMID: 29589097
DOI: 10.1007/s00401-018-1841-z

[…] reads in the BAM file and the number of reads mapping to the VNTR core sequence (chr19:1049514–1049953 [hg19]), which excludes sequencing reads aligning to the VNTR breakpoints, were calculated with Rsamtools []. Individuals with very low coverage (≤ 5 VNTR sequencing reads) were not included. VNTR coverage was then normalized by division by the total number of reads for that sample. Association […]

call_split

Developing a Bacteroides System for Function Based Screening of DNA from the Human Gut Microbiome

2018
mSystems
PMCID: 5872301
PMID: 29600285
DOI: 10.1128/mSystems.00195-17
call_split See protocol

[…] annotations were obtained for contigs of interest using RAST (). Regions of similarity between host and clone DNA were identified using Mauve (). Data analyses were performed in R, including packages Rsamtools, Gviz, ape, and genoPlotR. […]

library_books

A spliced latency associated VZV transcript maps antisense to the viral transactivator gene 61

2018
Nat Commun
PMCID: 5862956
PMID: 29563516
DOI: 10.1038/s41467-018-03569-2

[…] sulting assemblies were visualized using a combination of Circos, Artemis, Tablet, SeqMonk (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/) software and custom R scripts making use of the Rsamtools and Gviz software packages.To confirm that enrichment for viral nucleic acids did not bias relative levels of viral gene transcription, transcripts per million counts were generated using Fe […]

library_books

ATACseqQC: a Bioconductor package for post alignment quality assessment of ATAC seq data

2018
BMC Genomics
PMCID: 5831847
PMID: 29490630
DOI: 10.1186/s12864-018-4559-3

[…] uctor packages are leveraged. Alignment results in BAM files are first efficiently imported into R for quality assessment as GenomicAlignments objects using the readBamFile or scanBam function in the Rsamtools [] and GenomicRanges [] packages. The bamQC function implemented in our package can be used to assess the quality of the alignments and to generate filtered BAM files by removing reads with […]

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