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？