yes i have made adapters file myself because i have not find the best file corresponding to ScripSeq-v2 protocol in trimmomatic manual, in ScripSeq-v2 protocol it was mentionned this adapter:
5' CAAGCAGAAGACGGCATACGAGAT index (NNNNNN) GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT3'
and in my read 1 you find the reverse as:
GATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGATCTCGTATGCCGTCTTCTGCTTG
i don't know if TruSeq3-PE-2.fa adapter file was the good option to clean my PE reads.
5' CAAGCAGAAGACGGCATACGAGAT index (NNNNNN) GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT3'
and in my read 1 you find the reverse as:
GATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGATCTCGTATGCCGTCTTCTGCTTG
i don't know if TruSeq3-PE-2.fa adapter file was the good option to clean my PE reads.
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