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Old 06-10-2014, 01:50 AM   #1
Romz34
Junior Member
 
Location: France, Montpellier

Join Date: Jun 2014
Posts: 3
Default Trimmomatic problem

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

Code:
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 :

Code:
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
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Old 06-10-2014, 02:34 AM   #2
mastal
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Location: uk

Join Date: Mar 2009
Posts: 667
Default

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.
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