Skip to content

How does the 'poly-a' parameter trim polyT in R2? #860

@falsetry1514

Description

@falsetry1514

This instruction is from the cutadapt documentation
On paired-end reads, --poly-a removes poly-A tails from R1 and poly-T “heads” from R2
But I can't make clear the orient in R2, it trim R2 polyT tail or R2 polyT head?
For example, this is a read strcture
5'-Barcode-fixed_suquence-polyT-insert_read-UMI-3'
so the FASTQ R1 sequense is Barcode-UMI-..., FASTQ R2 sequence is UMI-insert_read-polyA
If I use --poly-a, it will trim R2, use as R1, polyA tail, but how cutadapt will trim at R1 (use as R2)?
Will it cut off the R1 tail or the R1 head?

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions