Adapter sequences for stranded paired end data

Question

[GR]

I am analyzing an SRA data. I want to trim the adapter sequences as the mapping rate is very low (29%). The oligonuceotides for the kit they have used seems to be the following. Can some one point out to me what could be the adapter sequence from this. This is stranded paired end data.

Thanks,
RT

NEXTflex™Sequence
RNA-SeqBarcode Adapter1 5'AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
5'GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGTATCTCGTATGCCGTCTTCTGCTTG
PCR Primer 1 5'AATGATACGGCGACCACCGAGATCTACACPCR 
Primer 2 5'CAAGCAGAAGACGGCATACGAGAT

Answer 1

[swbarnes2]

I'd run your fastqs thought fastqc. That will identify what adapter sequences, if any, need to be removed.

[GR]

FASTQC does not complaint about the adapter sequences. If there are no adapter sequence why my mapping rates are that low?