QC3 protocols

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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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Publication for QC3

QC3 in pipelines

 (7)
2018
PMCID: 5793181
PMID: 29320459
DOI: 10.3390/genes9010029

[…] data analysis pipeline tiger [] for srna sequencing data processing. cutadapt [] was used to trim 3′ adapters for raw reads. multi-perspective quality control [] on raw data was performed using qc3 []. all reads with length less than 16 nucleotides were discarded. the adaptor-trimmed reads were formatted into a non-redundant fastq file, where the read sequence and copy number was recorded […]

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 […]

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

[…] 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 […]

2016
PMCID: 5059559
PMID: 27774452
DOI: 10.1155/2016/9837310

[…] 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, […]

2015
PMCID: 4518285
PMID: 26197299
DOI: 10.1038/ncomms8715

[…] generated and sequenced at a cluster density of 950,000 clusters per mm2., multiple stages of quality control (qc) on sequencing data was carried out. raw data and alignment qc were performed using qc3 (ref. ), and expression analyses were carried out using multirankseq. all data passed qc. raw data were aligned with tophat 2 against mouse mm10 genome, and read count data were obtained using […]

QC3 in publications

 (8)
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 […]

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 […]

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 […]

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 […]

PMCID: 4536593
PMID: 26271746
DOI: 10.1186/s12864-015-1709-8

[…] end (2x50 bp) reads per sample., the rnaseq data went through multiple stages of thorough quality control as recommended by guo et al. []. raw data and alignment quality control were performed using qc3 [], and gene quantification quality control was conducted using multirankseq []. raw data were aligned with tophat2 [] against mouse mm10 reference genome, and read counts per gene were obtained […]

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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