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Old 05-21-2013, 12:11 AM   #1
Pengfei Liu
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!
Pengfei Liu is offline   Reply With Quote
Old 05-21-2013, 01:17 AM   #2
Senior Member
Location: uk

Join Date: Mar 2009
Posts: 667
Default standard of clean data

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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