Bix Command line

Trimmomatic

Module:

module load app/ Trimmomatic/0.36

Run Software:

PE data – writing to a directory called “trimmed” :

java -jar /apps/Trimmomatic/0.36/trimmomatic-0.36.jar PE Read1.fq Read2.fq trimmed/Read1_trim_p.fq trimmed/Read1_trim_unp.fq trimmed/Read2_trim_p.fq trimmed/Read2_trim_unp.fq …….. ”options”

SE data – writing to a directory called “trimmed” :

java -jar /apps/Trimmomatic/0.36/trimmomatic-0.36.jar SE Read1.fq Read1_trimm.fq …………. “options” 

Options: 

SLIDINGWINDOW:3:20

ILLUMINACLIP: TruSeq3-SE:2:30:10