37 lines
722 B
Bash
37 lines
722 B
Bash
#!/bin/bash
|
|
|
|
# reference: http://www.usadellab.org/cms/?page=trimmomatic
|
|
|
|
|
|
module load Trimmomatic
|
|
|
|
|
|
# (Example) Paired end
|
|
java -jar $EBROOTTRIMMOMATIC/trimmomatic.jar PE \
|
|
-phred33 \
|
|
input_forward.fq.gz \
|
|
input_reverse.fq.gz \
|
|
output_forward_paired.fq.gz \
|
|
output_forward_unpaired.fq.gz \
|
|
output_reverse_paired.fq.gz \
|
|
output_reverse_unpaired.fq.gz \
|
|
ILLUMINACLIP: TruSeq3-PE.fa:2:30:10 \
|
|
LEADING:3 \
|
|
TRAILING:3 \
|
|
SLIDINGWINDOW:4:25 \
|
|
HEADCROP:8 \
|
|
MINLEN:50
|
|
|
|
|
|
# (Example) Single end
|
|
java -jar $EBROOTTRIMMOMATIC/trimmomatic.jar SE \
|
|
-phred33 \
|
|
input.fq.gz \
|
|
output.fq.gz \
|
|
ILLUMINACLIP:TruSeq3-SE:2:30:10 \
|
|
LEADING:3 \
|
|
TRAILING:3 \
|
|
SLIDINGWINDOW:4:15 \
|
|
HEADCROP:8 \
|
|
MINLEN:50
|