Correct cutadapt parameters for polyA/T tail trimming

Parameters for polyA/T trimming with cutadapt are currently set in a wrong way. The following parameters should be used for different library types:

• paired-end/ 1st read ANTISENSE, 2nd read SENSE: -g TTTTTTTTTT, -A AAAAAAAAAA
• paired-end/ 1st read SENSE, 2nd read ANTISENSE: -a AAAAAAAAAA, -G TTTTTTTTTT
• single-end/ read ANTISENSE: -g TTTTTTTTTT
• single-end/ read SENSE: -a AAAAAAAAAA (this case seems to be implemented correctly)

Here is the explanation based on the preparation of the library for Illumina TruSeq sequencing (original document can be found here: https://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/samplepreps_truseq/truseq-stranded-total-rna-workflow/truseq-stranded-total-rna-workflow-reference-1000000040499-00.pdf). In the figure I additionally included possible locations of polyA/T stretches.