2.4 years ago by
This is not really a Galaxy question, but this help from Illumina should help. If what I know is still current, this protocol can result in artifact at both ends of the sequence (it depends on how long the reads are - these are always present if the construct was created correctly, but the full insert and index plus both ends are not always fully sequenced). That means that the reverse compliment should be checked for. https://support.illumina.com/sequencing/sequencing_kits/truseq-small-rna-kit/questions.html
The Illumina publications in the Galaxy 101 can also help with understanding how these technologies function:
Those noted, FastQC can be a very useful tool for finding overrepresented sequences. Cutadapt (available in the Tool Shed for use in a local/cloud Galaxy) is a popular tool for removal. Real library prep is not always perfect and it is best to check instead of just trusting that all is as expected from the protocol.
Illumina has historically not wanted proprietary sequences published online. Rather, they prefer to share this directly with customers. These are still around on various forums, but because of that, we are going to modify your post to remove the sequences listed.
Hopefully this helps! Jen, Galaxy team