1 - I'm analysing RNA-seq data from a publication that says adapters used are Truseq. I want to trim adapters from this data with trimmomatic, but in 'adapters' folder in trimmomatic there're several files with 'truseq' in the name: 'TruSeq2-PE.fa', 'TruSeq2-SE.fa', 'TruSeq3-PE-2.fa', 'TruSeq3-PE.fa' and 'TruSeq3-SE.fa'. Which of those files should be used?all?
2 - Also, why does TruSeq Index Adapter sequence in trimmomatic 'TruSeq3-SE.fa' file has an extra 'A' nucleotide at the beginning of the sequence:
when comparing with same adapter in adapter sequences' pdf provided by Illuminia (page 25): https://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/experiment-design/illumina-adapter-sequences-1000000002694-06.pdf ?
3 - Why is the TruSeq Universal Adapter in trimmomatic:
the reverse complement of the 3' part of same adapter in pdf provided by Illuminia (page 25)?
TruSeq Universal Adapter 5’ AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
4 - What are the different index underlined in adapter sequences provided by Illuminia?