regarding reamove the adopters

[deepika123]

Hello,

I have paired end illumina sequencing data. Can anyone tell me that which tool is good for adopter removal. I used Fastx tool but i am not getting -Q in this tool. i think it is a platform idetifier. Can anyone also describe -Q.

thanks in advance

[dpryan]

Give trimmomatic or trim_galore a try. The fastx tools don't deal will with paired-end reads (they tend to desync the files).

[atcghelix]

I like scythe for identifying and trimming adapter contamination: https://github.com/vsbuffalo/scythe

I know more people who use trimmomatic, though.

[bioBob]

Hi,

We had set of custom scripts, but have now switched to ea-utils. I like some of the options a bit better than fastx.

Bob

[SES]

cutadapt is a very efficient and flexible tool for adapter trimming. By the way, trim_galore is a script that runs cutadapt.

[deepika123]

if we do not know the sequence of adopter then which tool is used????? In cutadapt, it ask for adopter sequence but i do not know the adopter sequence? is there any solution for it ?

[bioBob]

You could try fastqc to look for enriched sequences or kmers.