Protocols

hiReadsProcessor specifications

Information


Unique identifier OMICS_16071
Name hiReadsProcessor
Software type Package/Module
Interface Command line interface
Restrictions to use None
Output data Parameters for demultiplexing and sample metadata.
Output format XLS, TXT
Operating system Unix/Linux, Mac OS
Programming languages R
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.16.0
Stability Stable
Requirements
methods, BiocGenerics, GenomicRanges, testthat, Biostrings, GenomicAlignments, dplyr, BiocParallel, knitr, R(>=3.0), hiAnnotator, sonicLength, rSFFreader, readxl
Maintained Yes

Download


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Versioning


No version available

Documentation


Maintainer


  • person_outline Nirav Malani

hiReadsProcessor citation

call_split

HIV latency and integration site placement in five cell based models

2013
Retrovirology
PMCID: 3765678
PMID: 23953889
DOI: 10.1186/1742-4690-10-90
call_split See protocol

[…] All datasets were processed using the hiReadsProcessor R package []. Adaptor trimmed reads were aligned to UCSC freeze hg19 using BLAT []. Genomic alignments were scored and required to start within the first three bases of a read with 98 […]

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