removing a part of sequence of all genes

Question

[Sara]

I have 3'-seq data and planning to remove polyA of all genes. I have aligned the reads but I do not know how to remove polyA at the end of genes. do you know how to do that?

[WouterDeCoster]

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Answer 1

[glihm]

Hello Sara,

you can use cutadapt to remove adapters (poly-A included). As the poly-A is usually found at the 3' end of reads, you can use the following as suggested by cutadapt documentation:

cutadapt -a "A{100}" -o output.fastq input.fastq