Entering edit mode
19 months ago
Ahmed
▴
10
i am trying to do trimming to my data after i do fastqc and determined that my data with bad quality score, but i get error my code is:
1- add my variable files and my adapter
f1="$Home/home/ngs/mouse_project/SRR5017134_Regular_Diet_Tumor_1.fastq.gz"
newf1="$Home/home/ngs/mouse_project/SRR5017134_Regular_Diet_Tumor_1.se.trim.fastq.gz"
adap="$CONDA_PREFIX/share/trimmomatic-0.39-2/adapters"
2-trimming step
trimmomatic SE -threads 1 -phred33 -trimlog trimLogFile -summary statsSummaryFile $f1 $newf1 \
ILLUMINACLIP:$adap/TruSeq3-SE.fa:2:30:10 SLIDINGWINDOW:4:15 MINLEN:36
i get there in the post title so what is the wrong?
You probably have corrupt fastq files. Are you able to run FastQC on them without getting an error?
You can use a fastq validation program (https://github.com/nunofonseca/fastq_utils use
fastq_info
) to check.Yes, I do I decided to do trimming on my data after running on fastqc