12. Dobin A, Davis CA, Schlesinger F, Drenkow J,
Zaleski C, Jha S, Batut P, Chaisson M, Gingeras
TR (2013) STAR: ultrafast universal RNA-seq
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2012/10/30. https://doi.org/10.1093/bio
informatics/bts635
13. Love MI, Huber W, Anders S (2014) Moderated estimation of fold change and dispersion
for RNA-seq data with DESeq2. Genome Biol
15(12):550. Epub 2014/12/18. https://doi.
org/10.1186/s13059-014-0550-8
14. Robinson MD, McCarthy DJ, Smyth GK
(2010) edgeR: a Bioconductor package for differential expression analysis of digital gene
expression
data.
Bioinformatics
26
(1):139–140. Epub 2009/11/17. https://
doi.org/10.1093/bioinformatics/btp616
15. Smyth GK (2005) Limma: linear models for
microarray data. In: Gentleman R, Carey VJ,
Huber W, Irizarry RA, Dudoit S (eds) Bioinformatics and computational biology solutions
using R and bioconductor. Springer New York,
New York, NY, pp 397–420
16. Rapaport F, Khanin R, Liang Y, Pirun M,
Krek A, Zumbo P, Mason CE, Socci ND,
Betel D (2015) Erratum to: Comprehensive
evaluation of differential gene expression analysis methods for RNA-seq data. Genome Biol
16:261. Epub 2015/11/26. https://doi.org/
10.1186/s13059-015-0813-z
17. Rapaport F, Khanin R, Liang Y, Pirun M,
Krek A, Zumbo P, Mason CE, Socci ND,
Betel D (2013) Comprehensive evaluation of
differential gene expression analysis methods
for RNA-seq data. Genome Biol 14(9):R95.
Epub 2013/09/12. https://doi.org/10.
1186/gb-2013-14-9-r95
18. Soneson C, Delorenzi M (2013) A comparison
of methods for differential expression analysis
of RNA-seq data. BMC Bioinformatics 14:91.
Epub 2013/03/19. https://doi.org/10.
1186/1471-2105-14-91
19. Schurch NJ, Schofield P, Gierlin ´ ski M, Cole C,
Sherstnev A, Singh V, Wrobel N, Gharbi K,
Simpson GG, Owen-Hughes T, Blaxter M,
Barton GJ (2016) How many biological
replicates are needed in an RNA-seq experiment and which differential expression tool
should you use? RNA 22(6):839–851.
https://doi.org/10.1261/rna.053959.115
20. Rustad T, Roberts D, Liao R, Sherman DR
(2008) Isolation of mycobacterial RNA. In:
Parish T, Brown AC (eds) Mycobacteria protocols, 2nd edn. Humana Press, London, UK
21. Andrews S. FastQC: a quality control tool for
high throughput sequence data. http://www.
bioinformatics.babraham.ac.uk/projects/
fastqc2010
22. Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina
sequence
data.
Bioinformatics
30
(15):2114–2120. https://doi.org/10.1093/
bioinformatics/btu170
23. Ewels P, Magnusson M, Lundin S, K€ aller M
(2016) MultiQC: summarize analysis results
for multiple tools and samples in a single
report. Bioinformatics 32(19):3047–3048.
https://doi.org/10.1093/bioinformatics/
btw354
24. Batut B. Quality Control (Galaxy Training
Materials) Online2020 [Jun 06 2020].
https://galaxyproject.github.io/training-mate
rial/topics/sequence-analysis/tutorials/qual
ity-control/tutorial.html
25. Robinson JT, Thorvaldsdottir H, Winckler W,
Guttman M, Lander ES, Getz G, Mesirov JP
(2011) Integrative genomics viewer. Nat Biotechnol 29(1):24–26. Epub 2011/01/12.
https://doi.org/10.1038/nbt.1754
26. Liao Y, Smyth GK, Shi W (2014) featureCounts: an efficient general purpose program
for assigning sequence reads to genomic features. Bioinformatics 30(7):923–930. Epub
2013/11/15. https://doi.org/10.1093/bio
informatics/btt656
27. Anders S, Pyl PT, Huber W (2015) HTSeq--a
Python framework to work with highthroughput sequencing data. Bioinformatics
31(2):166–169. https://doi.org/10.1093/
bioinformatics/btu638
512
Shuyi Ma et al.
Zaleski C, Jha S, Batut P, Chaisson M, Gingeras
TR (2013) STAR: ultrafast universal RNA-seq
aligner. Bioinformatics 29(1):15–21. Epub
2012/10/30. https://doi.org/10.1093/bio
informatics/bts635
13. Love MI, Huber W, Anders S (2014) Moderated estimation of fold change and dispersion
for RNA-seq data with DESeq2. Genome Biol
15(12):550. Epub 2014/12/18. https://doi.
org/10.1186/s13059-014-0550-8
14. Robinson MD, McCarthy DJ, Smyth GK
(2010) edgeR: a Bioconductor package for differential expression analysis of digital gene
expression
data.
Bioinformatics
26
(1):139–140. Epub 2009/11/17. https://
doi.org/10.1093/bioinformatics/btp616
15. Smyth GK (2005) Limma: linear models for
microarray data. In: Gentleman R, Carey VJ,
Huber W, Irizarry RA, Dudoit S (eds) Bioinformatics and computational biology solutions
using R and bioconductor. Springer New York,
New York, NY, pp 397–420
16. Rapaport F, Khanin R, Liang Y, Pirun M,
Krek A, Zumbo P, Mason CE, Socci ND,
Betel D (2015) Erratum to: Comprehensive
evaluation of differential gene expression analysis methods for RNA-seq data. Genome Biol
16:261. Epub 2015/11/26. https://doi.org/
10.1186/s13059-015-0813-z
17. Rapaport F, Khanin R, Liang Y, Pirun M,
Krek A, Zumbo P, Mason CE, Socci ND,
Betel D (2013) Comprehensive evaluation of
differential gene expression analysis methods
for RNA-seq data. Genome Biol 14(9):R95.
Epub 2013/09/12. https://doi.org/10.
1186/gb-2013-14-9-r95
18. Soneson C, Delorenzi M (2013) A comparison
of methods for differential expression analysis
of RNA-seq data. BMC Bioinformatics 14:91.
Epub 2013/03/19. https://doi.org/10.
1186/1471-2105-14-91
19. Schurch NJ, Schofield P, Gierlin ´ ski M, Cole C,
Sherstnev A, Singh V, Wrobel N, Gharbi K,
Simpson GG, Owen-Hughes T, Blaxter M,
Barton GJ (2016) How many biological
replicates are needed in an RNA-seq experiment and which differential expression tool
should you use? RNA 22(6):839–851.
https://doi.org/10.1261/rna.053959.115
20. Rustad T, Roberts D, Liao R, Sherman DR
(2008) Isolation of mycobacterial RNA. In:
Parish T, Brown AC (eds) Mycobacteria protocols, 2nd edn. Humana Press, London, UK
21. Andrews S. FastQC: a quality control tool for
high throughput sequence data. http://www.
bioinformatics.babraham.ac.uk/projects/
fastqc2010
22. Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina
sequence
data.
Bioinformatics
30
(15):2114–2120. https://doi.org/10.1093/
bioinformatics/btu170
23. Ewels P, Magnusson M, Lundin S, K€ aller M
(2016) MultiQC: summarize analysis results
for multiple tools and samples in a single
report. Bioinformatics 32(19):3047–3048.
https://doi.org/10.1093/bioinformatics/
btw354
24. Batut B. Quality Control (Galaxy Training
Materials) Online2020 [Jun 06 2020].
https://galaxyproject.github.io/training-mate
rial/topics/sequence-analysis/tutorials/qual
ity-control/tutorial.html
25. Robinson JT, Thorvaldsdottir H, Winckler W,
Guttman M, Lander ES, Getz G, Mesirov JP
(2011) Integrative genomics viewer. Nat Biotechnol 29(1):24–26. Epub 2011/01/12.
https://doi.org/10.1038/nbt.1754
26. Liao Y, Smyth GK, Shi W (2014) featureCounts: an efficient general purpose program
for assigning sequence reads to genomic features. Bioinformatics 30(7):923–930. Epub
2013/11/15. https://doi.org/10.1093/bio
informatics/btt656
27. Anders S, Pyl PT, Huber W (2015) HTSeq--a
Python framework to work with highthroughput sequencing data. Bioinformatics
31(2):166–169. https://doi.org/10.1093/
bioinformatics/btu638
512
Shuyi Ma et al.