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Bacterial RNASeq Expression profiles and genome size
Would some one guide me on how many million reads (50 bp, no pair ends) would be considered as 'safe' if objective is to get expression profile of the entire genome of Salmonella strain (~4.5 Mbp genome size). Thank you all in advance!
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I would consider 6-10m a good target to start with. We found sequencing to be better than chips in the past, even with <500k reads.
Frank S, Klockgether J, Hagendorf P, Geffers R, Schöck U, Pohl T, Davenport CF, Tümmler B.
Pseudomonas putida KT2440 genome update by cDNA sequencing and microarray transcriptomics.
Environ Microbiol. 2011 Feb 28. PMID: 21355971
Watch out for rRNA (95% of reads map there!).
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