Oligo Sequences
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Illumina HiSeqIllumina
rRNA bacterial gene and ITS fungal metagenomics primers
Blunt-end ligation with PCR addition of indexes
Some simple commands to use to search for adaptor-dimers:
In Illumina data:
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grep -c GATCGGAAGA <filename.fastq>
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This works for a standard Illumina genomic DNA library made with TruSeq V3 Y adaptors, and since the Y adaptors are RC's on each end, works equally well for read 1 and read 2.
For small-rna library/single stranded RNA library, The previous command will work for read 21. For read 12, use something like:
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grep -c 'ATCGTCGGAC' <filename.fastq> |