MAP-RSeq: Mayo Analysis Pipeline for RNA sequencing

BMC Bioinformatics

Volumn 15, Issue 1, 2014, Pages

  Kalari, Krishna R ^a   Nair, Asha A ^a   Bhavsar, Jaysheel D ^a   O'Brien, Daniel R ^a   Davila, Jaime I ^a   Bockol, Matthew A ^a   Nie, Jinfu ^a   Tang, Xiaojia ^a   Baheti, Saurabh ^a   Doughty, Jay B ^a   Middha, Sumit ^a   Sicotte, Hugues ^a   Thompson, Aubrey E ^b   Asmann, Yan W ^b   Kocher, Jean Pierre A ^a  

^a MAYO CLINIC   (United States)

^b MAYO CLINIC   (United States)

Author keywords

Bioinformatics workflow; Exon counts; Expressed single nucleotide variants; Fusion transcripts; Gene expression; RNA Seq; RNA Seq reports; Transcriptomic sequencing

Indexed keywords

BIOINFORMATICS; DIAGNOSIS; GENE EXPRESSION; NUCLEOTIDES; RESEARCH;

EXON COUNTS; RNA-SEQ; RNA-SEQ REPORTS; SINGLE NUCLEOTIDES; TRANSCRIPTOMIC SEQUENCING;

RNA;

ARTICLE; COMPUTER PROGRAM; EXON; GENE EXPRESSION PROFILING; GENETICS; GENOMICS; HEALTH CARE FACILITY; HIGH THROUGHPUT SEQUENCING; HUMAN; METHODOLOGY; NUCLEOTIDE SEQUENCE; SEQUENCE ANALYSIS;

BASE SEQUENCE; EXONS; GENE EXPRESSION PROFILING; GENOMICS; HEALTH FACILITIES; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; SEQUENCE ANALYSIS, RNA; SOFTWARE;

EID: 84902945763     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-15-224     Document Type: Article

References (36)

1. Barrett CL, Schwab RB, Jung H, Crain B, Goff DJ, Jamieson CHM, Thistlethwaite PA, Harismendy O, Carson DA, Frazer KA. Transcriptome sequencing of tumor subpopulations reveals a spectrum of therapeutic options for squamous cell lung cancer. PLoS One 2013, 8(3):e58714. 10.1371/journal.pone.0058714, 3604164, 23527012.
2. Chen YH, Souaiaia T, Chen T. PerM: efficient mapping of short sequencing reads with periodic full sensitive spaced seeds. Bioinformatics 2009, 25(19):2514-2521. 10.1093/bioinformatics/btp486, 2752623, 19675096.
3. Head SR, Mondala T, Gelbart T, Ordoukhanian P, Chappel R, Hernandez G, Salomon DR. RNA purification and expression analysis using microarrays and RNA deep sequencing. Methods Mol Biol 2013, 1034:385-403. 10.1007/978-1-62703-493-7_25, 23775753.
4. Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 2010, 26(1):139-140. 10.1093/bioinformatics/btp616, 2796818, 19910308.
5. Wang K, Singh D, Zeng Z, Coleman SJ, Huang Y, Savich GL, He X, Mieczkowski P, Grimm SA, Perou CM, MacLeod JN, Chiang DY, Prins JF, Liu J. MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery. Nucleic Acids Res 2010, 38(18):e178. 10.1093/nar/gkq622, 2952873, 20802226.
6. Goncalves A, Tikhonov A, Brazma A, Kapushesky M. A pipeline for RNA-seq data processing and quality assessment. Bioinformatics 2011, 27(6):867-869. 10.1093/bioinformatics/btr012, 3051320, 21233166.
7. Habegger L, Sboner A, Gianoulis TA, Rozowsky J, Agarwal A, Snyder M, Gerstein M. RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summaries. Bioinformatics 2011, 27(2):281-283. 10.1093/bioinformatics/btq643, 3018817, 21134889.
8. Qi J, Zhao FQ, Buboltz A, Schuster SC. inGAP: an integrated next-generation genome analysis pipeline. Bioinformatics 2010, 26(1):127-129. 10.1093/bioinformatics/btp615, 2796817, 19880367.
9. Wang Y, Mehta G, Mayani R, Lu JX, Souaiaia T, Chen YH, Clark A, Yoon HJ, Wan L, Evgrafov OV, Knowles JA, Deelman E, Chen T. RseqFlow: workflows for RNA-Seq data analysis. Bioinformatics 2011, 27(18):2598-2600. 3167055, 21795323.
10. MAP-RSeq website. [http://bioinformaticstools.mayo.edu/research/maprseq/].
11. Virtual Box download webpage. [https://www.virtualbox.org/wiki/Downloads].
12. CGHub webpage. [https://cghub.ucsc.edu/].
13. Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 2010, 26(6):841-842. 10.1093/bioinformatics/btq033, 2832824, 20110278.
14. Kent WJ. BLAT-the BLAST-like alignment tool. Genome Res 2002, 12(4):656-664. 10.1101/gr.229202. Article published online before March 2002, 187518, 11932250.
15. Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009, 10(3):R25. 10.1186/gb-2009-10-3-r25, 2690996, 19261174.
16. Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA. Circos: An information aesthetic for comparative genomics. Genome Res 2009, 19(9):1639-1645. 10.1101/gr.092759.109, 2752132, 19541911.
17. FastQC website. [http://www.bioinformatics.babraham.ac.uk/projects/fastqc/].
18. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA. The genome analysis toolkit: a map reduce framework for analyzing next-generation DNA sequencing data. Genome Res 2010, 20(9):1297-1303. 10.1101/gr.107524.110, 2928508, 20644199.
19. Anders S, Pyl PT, Huber W. HTSeq - A Python framework to work with high-throughput sequencing data. bioRxiv preprintbioRxiv preprint 2014,
20. Picard Tools webpage. [http://picard.sourceforge.net].
21. Wang LG, Wang SQ, Li W. RSeQC: quality control of RNA-seq experiments. Bioinformatics 2012, 28(16):2184-2185. 10.1093/bioinformatics/bts356, 22743226.
22. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. The Sequence Alignment/Map format and SAMtools. Bioinformatics 2009, 25(16):2078-2079. 10.1093/bioinformatics/btp352, 2723002, 19505943.
23. Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 2009, 25(9):1105-1111. 10.1093/bioinformatics/btp120, 2672628, 19289445.
24. Egan JB, Barrett MT, Champion MD, Middha S, Lenkiewicz E, Evers L, Francis P, Schmidt J, Shi CX, Van Wier S, Badar S, Ahmann G, Kortuem KM, Boczek NJ, Fonseca R, Craig DW, Carpten JD, Borad MJ, Stewart AK. Whole genome analyses of a well-differentiated liposarcoma reveals novel SYT1 and DDR2 Rearrangements. PLoS One 2014, 9(2):e87113. 10.1371/journal.pone.0087113, 3914808, 24505276.
25. Norton N, Sun Z, Asmann YW, Serie DJ, Necela BM, Bhagwate A, Jen J, Eckloff BW, Kalari KR, Thompson KJ, Carr JM, Kachergus JM, Geiger XJ, Perez EA, Thompson EA. Gene expression, single nucleotide variant and fusion transcript discovery in archival material from breast tumors. PLoS One 2013, 8(11):e81925. 10.1371/journal.pone.0081925, 3838386, 24278466.
26. Sakuma T, Davila JI, Malcolm JA, Kocher JP, Tonne JM, Ikeda Y. Murine leukemia virus uses NXF1 for nuclear export of spliced and unspliced viral transcripts. J Virol 2014,
27. Liao Y, Smyth GK, Shi W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 2014, 30(7):923-930. 10.1093/bioinformatics/btt656, 24227677.
28. Cufflink index and annotation. [http://cufflinks.cbcb.umd.edu/igenomes.html].
29. Grant GR, Farkas MH, Pizarro AD, Lahens NF, Schug J, Brunk BP, Stoeckert CJ, Hogenesch JB, Pierce EA. Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM). Bioinformatics 2011, 27(18):2518-2528. 3167048, 21775302.
30. Hardcastle TJ, Kelly KA. baySeq: empirical Bayesian methods for identifying differential expression in sequence count data. BMC Bioinform 2010, 11:422.
31. Anders S, Huber W. Differential expression analysis for sequence count data. Genome Biol 2010, 11(10):R106. 10.1186/gb-2010-11-10-r106, 3218662, 20979621.
32. Smyth GK. Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 2004, 3:Article 3.
33. Soneson C, Delorenzi M. A comparison of methods for differential expression analysis of RNA-seq data. BMC Bioinform 2013, 14:91.
34. Seyednasrollah F, Laiho A, Elo LL. Comparison of software packages for detecting differential expression in RNA-seq studies. Brief Bioinform 2013,
35. Rapaport F, Khanin R, Liang Y, Pirun M, Krek A, Zumbo P, Mason CE, Socci ND, Betel D. Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data. Genome Biol 2013, 14(9):R95. 10.1186/gb-2013-14-9-r95, 4054597, 24020486.
36. Kim D, Salzberg SL. TopHat-Fusion: an algorithm for discovery of novel fusion transcripts. Genome Biol 2011, 12(8):1.