Oligo Sequences
Roche 454
ABI SOLiD & Life Tech 5500XL
Illumina HiSeq
Some simple commands to use to search for adaptor-dimers:
In Illumina data:
grep -c GATCGGAAGA <filename.fastq>
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, The previous command will work for read 2. For read 1,
grep -c 'ATCGTCGGAC' <filename.fastq>
