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OpenGene
Option for overrepresented sequence
There is an option for overrepresented sequence analysis. If there is an option for trimming overrepresented sequence?
It's not reasonable to trim/filter overrepresented sequence.
If you want to remove deduplicated reads, use --dedup
I just want to trim my contaminate—overrepresented TSO, so I want to know whether there is an option to define sequence by
myself, like cutadapt.
I have another problem with fastp. While I input option, for example, -x for trimming ployx, I got the warning: undefined option. The same way of these option with warning—undefined option is that they can be found in fastp Github, but can't be found in the outfile while I input fastp -h.
Can you share cutadapt command? What's your fastp version? This is my fastp script: -q 10 -u 40 -n 10 -f 9 -3 -W 4 -M 10
-g -c -w 8
--trim_poly_x \ #this option will be warning -Y \ #this option will be warning --overrepresentation_analysis
And my fastp version is
