What is the difference between transcriptome sequencing and ESTs? does it make sense to map my transcriptome sequencing reads to an EST database of the same organism?
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ESTs were very popular in pre-NGS days, they were based on Sanger sequencing of cDNA ends (5' or 3' or both). Thus they give you somewhat similar information, less reads, but longer reads, derived from cDNAs. Transcriptome sequencing or RNA-Seq is based on shattering of RNA into 200-300bp fragments and then short-read sequencing of those fragments, and thus can potentially cover the entire transcript.
If you are working on an organism for which no genome is available, you could check your RNA-Seq reads by mapping them to ESTs. This will give you an idea of how complete your RNA-Seq library is (how many ESTs are covered at 100%?).
Bear in mind that you could assemble both your ESTs and RNA-Seq reads into longer contigs using de novo assembly tools if you are aiming to discover genes.--------------------------------------
Elia Stupka
Co-Director and Head of Unit
Center for Translational Genomics and Bioinformatics
San Raffaele Scientific Institute
Via Olgettina 58
20132 Milano
Italy
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