single end Trimmomatic
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Entering edit mode
5 weeks ago
gina02 ▴ 30

I've got a sra file in fastq format and I need to run single end Trimmomatic on the file. I've downloaded Trimmomatic in a new environment using conda command conda create -n trimmomatic trimmomatic the command I used for executing the function is :

trimmomatic SE -threads 4 SRR12304924_1.fastq/SRR12304924.trimmed.fastq\HEADCROP:19

the output I get is

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

what command should I use?

SE Trimmomatic • 201 views
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Entering edit mode
5 weeks ago
GenoMax 109k

You should use

trimmomatic SE -threads 4 SRR12304924_1.fastq SRR12304924.trimmed.fastq HEADCROP:19

If you need to trim adapters then you will need to provide them via ILLUMINACLIP option.

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Entering edit mode

got it thanks

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