Can I use TruSeq2-SE.fa blindly given in Trimmomatic?

Question

[akshay_ware]

Hi,

I am working on small RNA-Seq data analysis, I have query regarding trimmomatic tool which widely used for adapter trimming from reads.

In the command below:

trimmomatic SE -phred33 input.fastq Out_trimmomatic.fastq ILLUMINACLIP:/trimmomatic-0.38-1/adapters/TruSeq3-SE.fa:2:30:10 LEADING:30 TRAILING:30 MINLEN:36

TruSeq3-SE.fa its given in software package, Can we use same for all RNA-seq data-sets? What is the purpose of 2:30:10 after the adapter file?

Thanks in Advance..!!

[GenoMax]

Can we use same for all RNA-seq data-sets?

What do you think? As the name suggests that file contains adapters specific for Illumina's TruSeq kit. If your libraries were prepared using a different kit then that file either will not work at all or will work suboptimally in case your kit adapters share sequence similarity with TruSeq adapters.

Answer 1

[cschu181]

From the Trimmomatic Website

Step options:

ILLUMINACLIP:<fastaWithAdaptersEtc>:<seed mismatches>:<palindrome clip threshold>:<simple clip threshold>

fastaWithAdaptersEtc: specifies the path to a fasta file containing all the adapters, PCR sequences etc. The naming of the various sequences within this file determines how they are used. See below.

seedMismatches: specifies the maximum mismatch count which will still allow a full match to be performed

palindromeClipThreshold: specifies how accurate the match between the two 'adapter ligated' reads must be for PE palindrome read alignment.

simpleClipThreshold: specifies how accurate the match between any adapter etc. sequence must be against a read.

So, you could just use it as is for any [RNAseq] data set with TruSeq2 adapters, but you might want to check your results and then tweak the parameters if it over- or undertrims.

Edit: reformatted quotation from Trimmomatic website to make it more legible Edit2: addressed TruSeq