Cutadapt 5' adapter

Question

[ashwini]

Hi,

I am using cutadapt to trim small RNA reads.

The following is the command used -

cutadapt -a TGGAATTCTCGGGTGCCAAGG -g TTCAGAGTTCTACAGTCCGACGATC -m 15 -M 51 --untrimmed-output=FILE_NAME IN.fastq > OUT.fastq

I have changed "U" in the actual adapter to "T" while using with -g option (RA5) and have found few reads with this adapter. Am I right in doing this?

The 5' and 3' adapters are http://supportres.illumina.com/documents/documentation/chemistry_documentation/experiment-design/illumina-customer-sequence-letter.pdf

RNA 5' Adapter (RA5), part # 15013205
5' GUUCAGAGUUCUACAGUCCGACGAUC

RNA 3' Adapter (RA3), part # 15013207
5' TGGAATTCTCGGGTGCCAAGG

Answer 1

[Fabio Marroni]

Yes, you are right.

Since you are actually sequencing cDNA, you will have T and not U.