QuickRNASeq protocols

View QuickRNASeq computational protocol

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chevron_left Read alignment Normalization SNP detection Alignment evaluation Read quality control Differential expression File format conversion Known transcript quantification Spliced read alignment Gene expression visualization Bioinformatics workflows chevron_right
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QuickRNASeq specifications

Information


Unique identifier OMICS_10985
Name QuickRNASeq
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data In addition to raw sequence reads in FASTQ format, the only other required inputs are a reference genome file in FASTA format and a corresponding gene annotation file in GTF (gene transfer format).
Input format FASTQ, GTF
Output data The dynamic visualization features enable end users to explore and digest RNA-seq data analyses results intuitively and interactively, and to gain deep insights into RNA-seq datasets.
Operating system Unix/Linux
Programming languages Javascript, Perl, R, Shell (Bash)
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.2
Stability Stable
Requirements
edgeR, reshape, ggplot
Maintained Yes

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Additional information


http://baohongz.github.io/QuickRNASeq/

Publications for QuickRNASeq

QuickRNASeq in pipeline

2018
PMCID: 5768180
PMID: 29367853
DOI: 10.3389/fimmu.2017.01938

[…] data are presented as reads per kilobase of transcript per million reads mapped (rpkm) (). the qc report, processed read count table, rpkm table, and interactive data exploring tool generated by quickrnaseq is available at https://baohongz.github.io/irf5_knockdown. we used homer () for pathway analysis as it contains a program for performing functional enrichment analysis from a list […]


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QuickRNASeq in publication

PMCID: 5768180
PMID: 29367853
DOI: 10.3389/fimmu.2017.01938

[…] motif comparison suite (meme suite 4.8) (). peaks were visualized using igv genome browser (). rna-seq data qc, read mapping by star (), read counting by featurecounts () were handled through the quickrnaseq pipeline developed at pfizer (). subsequently, edger was used to determine differentially expressed genes; a p-value ≤ 0.05 and a false discovery rate (fdr) <0.05 […]


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QuickRNASeq institution(s)
Early Clinical Development, Pfizer Worldwide R&D, Cambridge, MA, USA; Inflammation & Immunology Research Unit, Pfizer WRD, Cambridge, MA, USA

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