rna seq data trim by trimmomatic

Question

[zh.khodadadi]

Hi every body

I am going to trim rna seq single end data(Illumina HiSeq 2000) by trimmomatics According to text:

sets of samples were trimmed and filtered with Trimmomatic to remove adapters with up to 2 mismatches, with a palindrome read alignment accuracy of 40 and a sequence match accuracy of 15. This program trimmed reads further by removing leading low-quality or N bases (below quality 3), removing trailing low-quality or N bases (below quality 3), and scanning each read with a 4-base-wide sliding window. The parameters were set for cutting when the average quality per base drops below 15 and then to drop any reads below 36 bases long*

Do these commands exactly refer to text? or need other commands? java -jar trimmomatic-0.36.jar SE -threads 8 -phred33 'path to fastq files' ILLUMINACLIP:TruSeq3-SE:2:30:10 SLIDINGWINDOW:4:15 MINLEN:36

[GenoMax]

Are you just looking for confirmation? If so, looks good.

[zh.khodadadi]

thanks No, I wanted to understand that are there other commands matches with this text??

[GenoMax]

The one you have above matches the text posted.

[zh.khodadadi]

Ok, thanks genomax2 .