1000 genomes raw data should be filtered?

[brukaro]

Hi! This is my first question, maybe somebody could help me.

Should I delete adaptor sequences from raw data reads from 1000 genomes?

Because it seems it contains some adaptors, but I cannot find which one.

Thank you!

[mastal]

How do you know the data contains adapters if you don't know the adapter sequence?

What platform/version are the data from?

For example, if it is Illumina data, then you would be able to use something like Trimmomatic, which comes with a file of adapter sequences for some versions of Illumina, to trim the adapters.

[brukaro]

@mastal
I applied FastQC to the data from ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data/
and the Illumina adaptors for Illumina reads to check

[brukaro]

if somebody would be interested
1000genome reads do not contain any adapters