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

Join Date: Jun 2014
Posts: 3
Default Trimmomatic problem


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 pair1.fastq unpair1.fastq pair2.fastq unpaire2.fastq
When I do that it just said :

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

Romz34 is offline   Reply With Quote
Old 06-10-2014, 02:34 AM   #2
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Location: uk

Join Date: Mar 2009
Posts: 667

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


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.
mastal is offline   Reply With Quote

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