Trimmomatic problem

[Romz34]

Hi,

i'm trying to run trimmomatic in pair-ended mode on my two fastq file, but it doesn't work without any error message. Here is what i'm running

java -jar trimmomatic-0.32.jar PE -phred33 input1.fast input2.fast pair1.fastq unpair1.fastq pair2.fastq unpaire2.fastq

When I do that it just said :

Usage: 
       PE [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] [-basein <inputBase> | <inputFile1> <inputFile2>] [-baseout <outputBase> | <outputFile1P> <outputFile1U> <outputFile2P> <outputFile2U>] <trimmer1>...
   or: 
       SE [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] <inputFile> <outputFile> <trimmer1>...

I tried to change different things, but nothing seems to work. I tried the "classpath" method which does the exact same thing.

Hope you can help ! thanks

Romain

[mastal]

I think the relevant part of the Usage error message that applies to the code you showed is

'<trimmer1>'.


You need to specify what trimming operations you want trimmomatic to do.
See the trimmomatic web page and the manual for a list of options.