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Protocols

QC3 specifications

Information


Unique identifier OMICS_05450
Name QC3
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Documentation


Publication for QC3

QC3 citations

 (11)
library_books

Palmitic Acid Induces Müller Cell Inflammation that is Potentiated by Co treatment with Glucose

2018
PMCID: 5889388
PMID: 29626212
DOI: 10.1038/s41598-018-23601-1

[…] technologies for advanced genomic analysis and research design (vangard) core performed sequence alignment and differential expression analyses. alignment and gene mapping was performed using qc3. differential expression was assessed using multirankseq, which uses the results of three statistical algorithms (deseq, edger, and bayseq) to more rigorously determine significantly altered gene […]

library_books

The Landscape of Small Non Coding RNAs in Triple Negative Breast Cancer

2018
PMCID: 5793181
PMID: 29320459
DOI: 10.3390/genes9010029

[…] of the reads at +1 or +2 positions from the start of the 5′ annotation of mirnas., the total rna-seq data was quality controlled following standard rna-seq quality control protocols [] using tools qc3 [], and alignment was carried out using bwa []. the nuclear genome we used is the human reference genome grch38. rna data alignment was performed by tophat2 []. read count per gene was extracted […]

call_split

Comprehensive evaluation of extracellular small RNA isolation methods from serum in high throughput sequencing

2017
PMCID: 5219650
PMID: 28061744
DOI: 10.1186/s12864-016-3470-z
call_split See protocol

[…] ex-srnas into four major categories: mirnas, isomirs, tdrs, and osrnas. cutadapt [] was used to trim 3’ adapters for raw reads. multi-perspective quality control [] on raw data was performed using qc3 []. all reads with lengths less than 16nts in length were discarded. the adaptor-trimmed reads were formatted into a non-redundant fastq file, where the read sequence and copy number was recorded […]

call_split

RNA Sequencing of Formalin Fixed, Paraffin Embedded Specimens for Gene Expression Quantification and Data Mining

2016
PMCID: 5059559
PMID: 27774452
DOI: 10.1155/2016/9837310
call_split See protocol

[…] rnaseq data was thoroughly quality-controlled at multiple stages (raw, alignment, and expression) following the recommendation by guo et al. []. raw data and alignment were quality-controlled using qc3 [], while expression data was quality-controlled using multirankseq []. alignments were performed using tophat 2 [] against the hg19 human reference genome. read counts for protein coding rnas, […]

library_books

Kinesin 5 inhibitor resistance is driven by kinesin 12

2016
PMCID: 5084272
PMID: 27091450
DOI: 10.1083/jcb.201507036

[…] independent reads). rnaseq data were thoroughly quality controlled at multiple stages of data processing as previously described (). raw data and alignment quality control were performed using qc3 (), and expression analysis was performed using multirankseq (). no quality issue was observed. raw data were aligned with tophat 2 () against human hg19 reference genome. gene expression […]

library_books

RNAseq by Total RNA Library Identifies Additional RNAs Compared to Poly(A) RNA Library

2015
PMCID: 4620295
PMID: 26543871
DOI: 10.1155/2015/862130

[…] into cdna and ligation of illumina paired-end oligo adapters to the cdna fragments. more detail of poly(a) library construction can be found at geo website., the raw data quality was examined using qc3 []. alignment against human genome reference hg19 was performed using tophat2 []. novel gene quantification was performed using cufflinks []. additional quality control was carried […]


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QC3 institution(s)
Vanderbilt Ingram Cancer Center, Center for Quantitative Sciences, Nashville, TN, USA; Center for Human Genetics Research, Vanderbilt University Medical Center, Nashville, TN, USA

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