Fastp

Question

[nishimalhotra2612]

Does fastp remove duplicated reads or not because I have been trying to remove the duplicate reads by using -D or --dedup but it's not working so can someone tell me if it's still available?

[GenoMax]

but it's not working

That does not tell us in what way is it not working. How did you determine that?

As long as you are using v.0.22 or above that feature should be available: https://github.com/OpenGene/fastp#deduplication

[nishimalhotra2612]

i used this command

fastp -i SRR13684098_1.fastq.gz -I SRR13684098_2.fastq.gz -o 098_1.fastq.gz -O 098_2.fastq.gz -D

and it shows undefined short option: -D

but mostly for enabling any feature we use this way only

sorry may be i am wrong also

[Pierre Lindenbaum]

what is your version of fastp ?

can you see the -D option in fastp --help

[nishimalhotra2612]

fastp 0.23.2

no i can't see i think its the latest version and even in github there is an option for removing duplications.

[GenoMax]

Use clumpify.sh then: Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files. And remove duplicates.

[nishimalhotra2612]

hey thanks for the suggestion but i figured it out as its rna-seq data there is no need to remove duplication as i might lose some important data