10. Baran-Gale J, Kurtz CL, Erdos MR et al
(2015) Addressing bias in small rna library
preparation for sequencing: a new protocol
recovers micrornas that evade capture by current methods. Front Genet 6:352
11. Hafner M, Renwick N, Farazi TA et al (2012)
Barcoded cdna library preparation for small rna
profiling by next-generation sequencing.
Methods 58:164–170
12. Hafner M, Renwick N, Brown M et al (2011)
Rna-ligase-dependent biases in mirna representation in deep-sequenced small rna cdna
libraries. RNA (New York, NY) 17:1697–1712
13. Raabe CA, Tang T-H, Brosius J et al (2013)
Biases in small rna deep sequencing data.
Nucleic Acids Res 42:1414–1426
14. Zhu H, Hu F, Wang R et al (2011) Arabidopsis
argonaute10 specifically sequesters mir166/
165 to regulate shoot apical meristem development. Cell 145:242–256
15. Zhang Z, Liu X, Guo X et al (2016) Arabidopsis ago3 predominantly recruits 24-nt small
rnas to regulate epigenetic silencing. Nat Plants
2:16049
16. Zhang Z, Hu F, Sung MW et al (2017) Riscinteracting clearing 3
0 -5
0 exoribonucleases
(rices) degrade uridylated cleavage fragments
to maintain functional risc in Arabidopsis thaliana. elife 6:e24466
17. Wang Z, Ma Z, Castillo-Gonza ´lez C et al
(2018) Swi2/snf2 atpase chr2 remodels
pri-mirnas via serrate to impede mirna production. Nature 557:516–521
18. Ma Z, Castillo-Gonzalez C, Wang Z et al
(2018) Arabidopsis serrate coordinates histone
methyltransferases atxr5/6 and rna processing
factor rdr6 to regulate transposon expression.
Dev Cell 45: 769–784 e766
19. Guo X, Ma Z, Zhang Z et al (2017) Small
rna-sequencing links physiological changes
and rddm process to vegetative-to-floral transition in apple. Front Plant Sci 8:873
20. Lee Y, Kim VN (2005) Preparation and analysis
of drosha. Rna silencing. Springer, pp 17–28
21. Kuksa PP, Amlie-Wolf A, Katanic ´ Z ˇ et al (2018)
Spar: Small rna-seq portal for analysis of
sequencing experiments. Nucleic Acids Res
46:W36–W42
22. Hoogstrate Y, Jenster G, Martens-Uzunova ES
(2014) Flaimapper: computational annotation
of small ncrna-derived fragments using rna-seq
high-throughput
data.
Bioinformatics
31:665–673
23. Wu X, Kim T-K, Baxter D et al (2017) Srnanalyzer—a flexible and customizable small rna
sequencing data analysis pipeline. Nucleic
Acids Res 45:12140–12151
24. Davis MPA, van Dongen S, Abreu-Goodger C
et al (2013) Kraken: a set of tools for quality
control and analysis of high-throughput
sequence data. Methods 63:41–49
25. Patel RK, Jain M (2012) Ngs qc toolkit: a
toolkit for quality control of next generation
sequencing data. PLoS One 7:e30619
26. Gordon A, Hannon G (2010) Fastx-toolkit.
FASTQ/A short-reads preprocessing tools
(unpublished)
http://hannonlab.cshl.edu/
fastx_toolkit 5
27. Martin M (2011) Cutadapt removes adapter
sequences from high-throughput sequencing
reads. EMBnet J 17:10–12
28. Jiang H, Lei R, Ding S-W et al (2014) Skewer:
a fast and accurate adapter trimmer for nextgeneration sequencing paired-end reads. BMC
Bioinform 15:182–182
29. Lohse M, Bolger AM, Nagel A et al (2012)
Robina: a user-friendly, integrated software
solution for rna-seq-based transcriptomics.
Nucleic Acids Res 40:W622–W627
30. Fonseca NA, Rung J, Brazma A et al (2012)
Tools for mapping high-throughput sequencing data. Bioinformatics 28:3169–3177
31. Langmead B, Trapnell C, Pop M et al (2009)
Ultrafast and memory-efficient alignment of
short DNA sequences to the human genome.
Genome Biol 10:R25
32. Li H, Handsaker B, Wysoker A et al (2009)
The sequence alignment/map format and samtools. Bioinformatics 25:2078–2079
33. Trapnell C, Roberts A, Goff L et al (2012)
Differential gene and transcript expression
analysis of rna-seq experiments with tophat
and cufflinks. Nat Protoc 7:562
34. Liao Y, Smyth GK, Shi W (2013) Featurecounts: an efficient general purpose program
for assigning sequence reads to genomic features. Bioinformatics 30:923–930
35. Pyl PT, Anders S, Huber W (2014) Htseq—a
python framework to work with highthroughput sequencing data. Bioinformatics
31:166–169
36. Dillies M-A, Rau A, Aubert J et al (2012) A
comprehensive evaluation of normalization
methods for illumina high-throughput rna
sequencing data analysis. Brief Bioinform
14:671–683
Identification and Quantification of sRNAs
253
(2015) Addressing bias in small rna library
preparation for sequencing: a new protocol
recovers micrornas that evade capture by current methods. Front Genet 6:352
11. Hafner M, Renwick N, Farazi TA et al (2012)
Barcoded cdna library preparation for small rna
profiling by next-generation sequencing.
Methods 58:164–170
12. Hafner M, Renwick N, Brown M et al (2011)
Rna-ligase-dependent biases in mirna representation in deep-sequenced small rna cdna
libraries. RNA (New York, NY) 17:1697–1712
13. Raabe CA, Tang T-H, Brosius J et al (2013)
Biases in small rna deep sequencing data.
Nucleic Acids Res 42:1414–1426
14. Zhu H, Hu F, Wang R et al (2011) Arabidopsis
argonaute10 specifically sequesters mir166/
165 to regulate shoot apical meristem development. Cell 145:242–256
15. Zhang Z, Liu X, Guo X et al (2016) Arabidopsis ago3 predominantly recruits 24-nt small
rnas to regulate epigenetic silencing. Nat Plants
2:16049
16. Zhang Z, Hu F, Sung MW et al (2017) Riscinteracting clearing 3
0 -5
0 exoribonucleases
(rices) degrade uridylated cleavage fragments
to maintain functional risc in Arabidopsis thaliana. elife 6:e24466
17. Wang Z, Ma Z, Castillo-Gonza ´lez C et al
(2018) Swi2/snf2 atpase chr2 remodels
pri-mirnas via serrate to impede mirna production. Nature 557:516–521
18. Ma Z, Castillo-Gonzalez C, Wang Z et al
(2018) Arabidopsis serrate coordinates histone
methyltransferases atxr5/6 and rna processing
factor rdr6 to regulate transposon expression.
Dev Cell 45: 769–784 e766
19. Guo X, Ma Z, Zhang Z et al (2017) Small
rna-sequencing links physiological changes
and rddm process to vegetative-to-floral transition in apple. Front Plant Sci 8:873
20. Lee Y, Kim VN (2005) Preparation and analysis
of drosha. Rna silencing. Springer, pp 17–28
21. Kuksa PP, Amlie-Wolf A, Katanic ´ Z ˇ et al (2018)
Spar: Small rna-seq portal for analysis of
sequencing experiments. Nucleic Acids Res
46:W36–W42
22. Hoogstrate Y, Jenster G, Martens-Uzunova ES
(2014) Flaimapper: computational annotation
of small ncrna-derived fragments using rna-seq
high-throughput
data.
Bioinformatics
31:665–673
23. Wu X, Kim T-K, Baxter D et al (2017) Srnanalyzer—a flexible and customizable small rna
sequencing data analysis pipeline. Nucleic
Acids Res 45:12140–12151
24. Davis MPA, van Dongen S, Abreu-Goodger C
et al (2013) Kraken: a set of tools for quality
control and analysis of high-throughput
sequence data. Methods 63:41–49
25. Patel RK, Jain M (2012) Ngs qc toolkit: a
toolkit for quality control of next generation
sequencing data. PLoS One 7:e30619
26. Gordon A, Hannon G (2010) Fastx-toolkit.
FASTQ/A short-reads preprocessing tools
(unpublished)
http://hannonlab.cshl.edu/
fastx_toolkit 5
27. Martin M (2011) Cutadapt removes adapter
sequences from high-throughput sequencing
reads. EMBnet J 17:10–12
28. Jiang H, Lei R, Ding S-W et al (2014) Skewer:
a fast and accurate adapter trimmer for nextgeneration sequencing paired-end reads. BMC
Bioinform 15:182–182
29. Lohse M, Bolger AM, Nagel A et al (2012)
Robina: a user-friendly, integrated software
solution for rna-seq-based transcriptomics.
Nucleic Acids Res 40:W622–W627
30. Fonseca NA, Rung J, Brazma A et al (2012)
Tools for mapping high-throughput sequencing data. Bioinformatics 28:3169–3177
31. Langmead B, Trapnell C, Pop M et al (2009)
Ultrafast and memory-efficient alignment of
short DNA sequences to the human genome.
Genome Biol 10:R25
32. Li H, Handsaker B, Wysoker A et al (2009)
The sequence alignment/map format and samtools. Bioinformatics 25:2078–2079
33. Trapnell C, Roberts A, Goff L et al (2012)
Differential gene and transcript expression
analysis of rna-seq experiments with tophat
and cufflinks. Nat Protoc 7:562
34. Liao Y, Smyth GK, Shi W (2013) Featurecounts: an efficient general purpose program
for assigning sequence reads to genomic features. Bioinformatics 30:923–930
35. Pyl PT, Anders S, Huber W (2014) Htseq—a
python framework to work with highthroughput sequencing data. Bioinformatics
31:166–169
36. Dillies M-A, Rau A, Aubert J et al (2012) A
comprehensive evaluation of normalization
methods for illumina high-throughput rna
sequencing data analysis. Brief Bioinform
14:671–683
Identification and Quantification of sRNAs
253