Skip to content

Latest commit

 

History

History
8 lines (7 loc) · 453 Bytes

3.Trimming.md

File metadata and controls

8 lines (7 loc) · 453 Bytes
Raw
# Trim reads
java -jar /services/tools/trimmomatic/0.38/trimmomatic-0.38.jar PE -phred33 SRRXXXXXXX_1.fastq SRRXXXXXXX_2.fastq SRRXXXXXXX_1_paired.fastq SRRXXXXXXX_1_unpaired.fastq SRRXXXXXXX_2_paired.fastq SRRXXXXXXX_2_unpaired.fastq MINLEN:36 SLIDINGWINDOW:4:15

# Look at the quality of the reads after trimming
/services/tools/fastqc/0.11.8/fastqc SRRXXXXXXX_1_paired.fastq
/services/tools/fastqc/0.11.8/fastqc SRRXXXXXXX_2_paired.fastq