I am a doctoral student starting my work in transcriptomes. My lab has never done it and we are venturing in the new era of transcriptome studies. I need help understanding what I am doing and how to analyze the data from deep sequencing?
I suggest you to visit this link: https://www.google.it/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&ved=0CDAQFjAA&url=http%3A%2F%2Fwww.qiagen.com%2Fresources%2FDownload.aspx%3Fid%3D%257B6910F167-E4AE-43A2-B87D-26A74C55A75C%257D%26lang%3Den%26ver%3D1&ei=0iudUeODOoT-PIbegMgJ&usg=AFQjCNF9P-Os9mKbAGQuezX6LhDE2qm2lg&sig2=Me0C2n_eEWfY7DNiFFzhYw&bvm=bv.46751780,d.bGE
another link: https://www.noble.org/Global/medicagohandbook/pdf/Transcriptomics.pdf
further link: http://www.systembio.com/downloads/Manual_Full_Spectrum_v6.pdf
Depending of the transcriptomics analysis that you want to do. Right now the most common menthodologies are microarrays and RNAseq, but RNAseq analysis is almost displacing the microarray analysis. For a comparison between both methodologies you can take a look to Marionni et al. 2008 (http://genome.cshlp.org/content/18/9/1509.short).
About RNAseq I recommend several sources:
*) Review articles such as Wang et al. 2008 (http://www.nature.com/nrg/journal/v10/n1/full/nrg2484.html), Strickler et al. 2012 (http://www.amjbot.org/content/99/2/257.long) or Mutz et al. 2013 (http://www.sciencedirect.com/science/article/pii/S0958166912001310).
*) Books, some general bioinformatics books contain a chapter for transcriptomics. for example: "Bioinformatics and Functional Genomics" by Pevsner contains a chapter for microarrays or "OMICS: Applications in Biomedical, Agricultural, and Environmental Sciences" by Barth contains a chapter for Next Generation Sequencing.
*) Courses material. For example BTI Bioinformatics course contains a block for RNAseq analysis (http://btiplantbioinfocourse.wordpress.com/2013-course/course-program/rnaseq-analysis/ or http://www.slideshare.net/aubombarely/rnaseq-analysis-19910448)
I can recommend: Nat Protoc. 2012 Mar 1;7(3):562-78. doi: 10.1038/nprot.2012.016. [MEDLINE] DOI: 10.1038/nprot.2012.016
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks.
Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L.
Hopefully that helps.
That is wonderful everyone. Thank you so much. I appreciate the help.
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