FastQC. http://www.bioinformatics.babraham.ac.uk/projects/fastqc.
Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29:15–21.
Article
CAS
Google Scholar
Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, Wei G, Chepelev I, Zhao K. High-resolution profiling of histone methylations in the human genome. Cell. 2007;129(4):823–37.
Article
CAS
Google Scholar
Yeo GW, Coufal NG, Liang TY, Peng GE, Fu XD, Gage FH. An RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cells. Nat Struct Mol Biol. 2009;16(2):130–7.
Article
CAS
Google Scholar
Hower V, Starfield R, Roberts A, Pachter L. Quantifying uniformity of mapped reads. Bioinformatics. 2012;28(20):2680–2.
Article
CAS
Google Scholar
Calviello L, Mukherjee N, Wyler E, Zauber H, Hirsekorn A, Selbach M, Landthaler M, Obermayer B, Ohler U. Detecting actively translated open reading frames in ribosome profiling data. Nat Methods. 2016;13(2):165–70.
Article
CAS
Google Scholar
Shin H, Liu T, Manrai AK, Liu XS. CEAS: cis-regulatory element annotation system. Bioinformatics. 2009;25(19):2605–6.
Article
CAS
Google Scholar
Sun Z, Evans J, Bhagwate A, Middha S, Bockol M, Yan H, Kocher JP. CAP-miRSeq: a comprehensive analysis pipeline for microRNA sequencing data. BMC Genomics. 2014;15:423.
Article
Google Scholar
Heinz S, Benner C, Spann N, Bertolino E, Lin YC, Laslo P, Cheng JX, Murre C, Singh H, Glass CK. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell. 2010;38(4):576–89.
Article
CAS
Google Scholar
Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010;26(6):841–2.
Article
CAS
Google Scholar
Neph S, Kuehn MS, Reynolds AP, Haugen E, Thurman RE, Johnson AK, Rynes E, Maurano MT, Vierstra J, Thomas S, Sandstrom R, Humbert R, Stamatoyannopoulos JA. BEDOPS: high-performance genomic feature operations. Bioinformatics. 2012;28(14):1919–20.
Article
CAS
Google Scholar
bam2x. https://github.com/nimezhu/bam2x.
Jiang Z, Yang J, Dai A, Wang Y, Li W, Xie Z. Ribosome profiling reveals translational regulation of mammalian cells in response to hypoxic stress. BMC Genomics. 2017;18(638).
Schmitz RJ, Schultz MD, Lewsey MG, O’Malley RC, Urich MA, Libiger O, Schork NJ, Ecker JR. Transgenerational epigenetic instability is a source of novel methylation variants. Science. 2011;334(6054):369–73.
Article
CAS
Google Scholar
Becker C, Hagmann J, Muller J, Koenig D, Stegle O, Borgwardt K, Weigel D. Spontaneous epigenetic variation in the Arabidopsis thaliana methylome. Nature. 2011;480(7376):245–9.
Article
CAS
Google Scholar
Reid DW, Shenolikar S, Nicchitta CV. Simple and inexpensive ribosome profiling analysis of mRNA translation. Methods. 2015.
Ingolia NT, Ga B, Rouskin S, McGeachy AM, Weissman JS. The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments. Nat Protoc. 2012;7:1534–50.
Article
CAS
Google Scholar
Choy JYH, Boon PLS, Bertin N, Fullwood MJ: A resource of ribosomal RNA-depleted RNA-Seq data from different normal adult and fetal human tissues. Scientific data 2015, 2:150063, [http://www.ncbi.nlm.nih.gov/pubmed/26594381, http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC4640133].
Ikegami K, Lieb JD. Integral nuclear pore proteins bind to pol III-transcribed genes and are required for pol III transcript processing in C. Elegans. Mol Cell. 2013;51(6):840–9.
Article
CAS
Google Scholar
Dieci G, Fiorino G, Castelnuovo M, Teichmann M, Pagano A. The expanding RNA polymerase III transcriptome. Trends Genet. 2007;23(12):614–22.
Article
CAS
Google Scholar
Thompson DM, Parker R. Cytoplasmic decay of intergenic transcripts in Saccharomyces cerevisiae. Mol Cell Biol. 2007;27:92–101.
Article
CAS
Google Scholar
Schulz D, Schwalb B, Kiesel A, Baejen C, Torkler P, Gagneur J, Soeding J, Cramer P. Transcriptome surveillance by selective termination of noncoding RNA synthesis. Cell. 2013;155(5):1075–87.
Article
CAS
Google Scholar
van Dijk EL, Chen CL, d’Aubenton Carafa Y, Gourvennec S, Kwapisz M, Roche V, Bertrand C, Silvain M, Legoix-Ne P, Loeillet S, Nicolas A, Thermes C, Morillon A. XUTs are a class of Xrn1-sensitive antisense regulatory non-coding RNA in yeast. Nature. 2011;475(7354):114–7.
Article
Google Scholar
Xu Z, Wei W, Gagneur J, Perocchi F, Clauder-Munster S, Camblong J, Guffanti E, Stutz F, Huber W, Steinmetz LM. Bidirectional promoters generate pervasive transcription in yeast. Nature. 2009;457(7232):1033–7.
Article
CAS
Google Scholar
Liao Y, Smyth GK, Shi W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. 2014;30(7):923–30.
Article
CAS
Google Scholar
Wang L, Wang S, Li W. RSeQC: quality control of RNA-seq experiments. Bioinformatics. 2012;28(16):2184–5.
Article
CAS
Google Scholar