**Author details**

Bijesh George, Vivekanand Ashokachandran, Aswathy Mary Paul and Reshmi Girijadevi\*

[11] Afgan E, Baker D, van den Beek M, Blankenberg D, Bouvier D, Cech M, et al. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016

Transcriptome Sequencing for Precise and Accurate Measurement of Transcripts and...

http://dx.doi.org/10.5772/intechopen.70026

167

[12] Lindner R, Friedel CC. A comprehensive evaluation of alignment algorithms in the con-

[13] Ewing B, Green P. Base-calling of automated sequencer traces using phred. II. Error

[14] Guttman M, Garber M, Levin JZ, Donaghey J, Robinson J, Adiconis X, et al. Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-

[15] Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y. RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays. Genome Research.

[16] Wang Z, Gerstein M, Snyder M. RNA-Seq: A revolutionary tool for transcriptomics.

[17] Wilhelm BT, Landry JR. RNA-Seq-quantitative measurement of expression through

[18] Katz Y, Wang ET, Airoldi EM, Burge CB. Analysis and design of RNA sequencing experiments for identifying isoform regulation. Nature Methods. 2010;**7**(12):1009-1015

[19] Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform

[20] Bahn JH, Lee JH, Li G, Greer C, Peng G, Xiao X. Accurate identification of A-to-I RNA editing in human by transcriptome sequencing. Genome Research. 2012;**22**(1):142-150

[21] Park E, Williams B, Wold BJ, Mortazavi A. RNA editing in the human ENCODE RNA-

[22] Peng Z, Cheng Y, Tan BC, Kang L, Tian Z, Zhu Y, et al. Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome. Nature Biotechnology.

[23] Ramaswami G, Zhang R, Piskol R, Keegan LP, Deng P, O'Connell MA, et al. Identifying RNA editing sites using RNA sequencing data alone. Nature Methods. 2013;**10**(2):128-132

[24] Cabili MN, Trapnell C, Goff L, Koziol M, Tazon-Vega B, Regev A, et al. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific

[25] Prensner JR, Iyer MK, Balbin OA, Dhanasekaran SM, Cao Q, Brenner JC, et al. Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA

implicated in disease progression. Nature Biotechnology. 2011;**29**(8):742-749

switching during cell differentiation. Nature Biotechnology. 2010;**28**(5):511-515

exonic structure of lincRNAs. Nature Biotechnology. 2010;**28**(5):503-510

massively parallel RNA-sequencing. Methods. 2009;**48**(3):249-257

update. Nucleic Acids Research. 2016;**44**(W1):W3-W10

text of RNA-seq. PLoS One. 2012;**7**(12):e52403

Nature Reviews Genetics. 2009;**10**(1):57-63

seq data. Genome Research. 2012;**22**(9):1626-1633

subclasses. Genes & Development. 2011;**25**(18):1915-1927

2008;**18**(9):1509-1517

2012;**30**(3):253-260

probabilities. Genome Research. 1998;**8**(3):186-194

\*Address all correspondence to: reshmisuresh@gmail.com

Cancer Research Program-9, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
