Recently we sequenced small RNA sequencing using Rapid Run platform. As the size of the small RNA ranges between 18 to 35bases. The reads from this run would have bases sequenced from the adapters and primers. I am planning to trim off the adapters and primers.
I am currently using Trimmomatic tool for trimming process. Along with the tool, I have a list of adapters in FASTA format. Within Trimmomatic tool, there is a folder named "Adapters". It has following files
In my case, I used "Illumina-SmallRNAAdapter.fa" and "Illumina-MultiplexingPrimer.fa" for trimming the reads.
RNA 3 Adapter TGGAATTCTCGGGTGCCAAGG
Do I need download any specific adapters for Illumina small RNA sequencing kit?
Illumina_Adapter_Full.txt IlluminaAdapter-PE.fa Illumina-MultiplexingPrimer.fa Illumina-SmallRNAAdapter.fa Illumina-TruSeqAdapter.fa
can any one provide these files link?
Files currently include with
trimmomaticshould cover all necessary Illumina adapters.
With small RNA kits there may be a kit specific adapter sequence so you should always check which kit was used and follow data processing instructions (if provided).