removing a part of sequence of all genes

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?

rna-seq

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updated 8.8 years ago by glihm

• written 8.8 years ago by Sara

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written 8.8 years ago by WouterDeCoster

1 answer

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

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written 8.8 years ago by glihm

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