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..!!




From the [Trimmomatic Website][1]

> Step options:
> 
> ILLUMINACLIP:&lt;fastaWithAdaptersEtc&gt;:&lt;seed mismatches&gt;:&lt;palindrome clip
> threshold&gt;:&lt;simple clip threshold&gt; 

> 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.

  [1]: http://www.usadellab.org/cms/?page=trimmomatic

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