Entering edit mode
16 months ago
salmon ▴ 10
I am using RNA sequence data (forward and reverse fastq sequence) for my pure culture bacteria. I used the following sickle code and I am getting empty trimmed file. I am not sure where I am going wrong
sickle pe -f Data/K1_R1.fastq -r Data/ K1_R2.fastq -t sanger -o K1_trimmed.fastq -p K2_trimmed.fastq -s qtrim.unparied.fastq -q 30 -l 130 Warning: PE file 2 is shorter than PE file 1. Disregarding rest of PE file 1. Result FastQ paired records kept: 0 (0 pairs) FastQ single records kept: 0 (from PE1: 0, from PE2: 0) FastQ paired records discarded: 0 (0 pairs) FastQ single records discarded: 0 (from PE1: 0, from PE2: 0)
I checked the Fastqc report of K1_R1 (Forward read) and K1_R2 (reverse read)as attached below for quality check.
I just want to let you know that sickle seems quite outdated. I’d go for trimmomatic or some other tools.
Agreed. I'd recommend
You are not likely to have sanger formatted data if this is recent data.
That message is odd. FastQC indicates that there are an equal number of reads in your files. I second jkim suggestion of trying a different program.
Thank you so much for your reply.