standard of clean data

[Pengfei Liu]

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!

[mastal]

standard of clean data

1. remove reads with adaptors

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