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Old 05-21-2013, 12:11 AM   #1
Pengfei Liu
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Location: Beijing

Join Date: Nov 2012
Posts: 16
Default standard of clean data

Hi all
I recently got my prokaryotes RNA-seq data report back. the standard filter steps of the raw data set by our local sequencing center is as following:
1. remove reads with adaptors
2. remove reads with unknown nucleotides larger than 10%
3. remove reads with low quality (more than 40% of the bases' qualities are less than 20)
4. Obtain clean reads

Is this suitable standard, is there any reference that discusses this topic, thanks!
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Old 05-21-2013, 01:17 AM   #2
mastal
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Location: uk

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Default standard of clean data

Quote:
Originally Posted by Pengfei Liu View Post

1. remove reads with adaptors
In general, one would trim the reads to remove the adapter sequence, not remove the entire read.
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