Question: Trimming Adapters for Illumina Small RNA Libraries
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gravatar for gkuffel22
2.7 years ago by
gkuffel22170
United States
gkuffel22170 wrote:

Does anyone know exactly which sequences I should be clipping on an Illumina Small RNA library before aligning? I have the Illumina Adapter letter which specifies the following but I am not sure if I just type these in as seen or if I need to take the reverse complement of the sequences:

TruSeq® Small RNA Sample Prep Kits 

(Sequence removed by moderator)

mirnaseq • 2.4k views
ADD COMMENTlink modified 2.7 years ago by Jennifer Hillman Jackson25k • written 2.7 years ago by gkuffel22170
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gravatar for Jennifer Hillman Jackson
2.7 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

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:
https://wiki.galaxyproject.org/Learn/GalaxyNGS101#Overview_of_NGS_technologies

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

ADD COMMENTlink written 2.7 years ago by Jennifer Hillman Jackson25k
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