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Old 12-03-2010, 01:35 PM   #1
harrike
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Location: St. Louis, MO

Join Date: Jun 2010
Posts: 29
Default [Small RNA sequencing] 10-12 M raw reads enough?

Hi, all,

I am a novice in solid deep sequencing. Months before I made several small RNA libraries using the SOLID total RNA seq Kit. The final concentrations of these libraries were relatively low (about 10 ng/ul), but they all reached the requirement for deep sequencing, and their ratio of 120-130bp/25-150bp, obtained by Agilent bioanalyzer, was above 50%. So we sent them to the sequencing company. The company helped us with the ePCR and sequencing. This week I got the sequencing results. Most libraries got about 10-12 M raw reads, which is lower than the supposed 16 M. Is 10-12 M reads enough for my following bioinformatic analysis? Will the results be accurate to reflect the transcript level of small RNAs in the plant ?

By the way, I used SOLID barcode primer in the library construction process

I hope someone here has related experience on small RNA deep sequencing, and is willing to share your knowledge with me? Thank a lot.

If anything confusing, let me know.
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