Hi, I am trying to run trimmomatic directly in the Trinity command, I am using the following:
trinity --seqType fq --max_memory 100G --left ~/Dp_RNAseq/raw_data/All_reads_R1.fastq --right ~/Dp_RNAseq/raw_data/All_reads_R2.fastq --CPU 8 --output ~/Dp_RNAseq/Trinity/ --quality_trimming_params "LEADING:2 TRAILING:2 MINLEN:25"
Doesn't matter how I type it, or the actual options I put in. Trinity doesn't seem to be able to read the parameters in the --quality_trimmin_params. I see getting the error:
"Error, do not understand options: TRAILING:2 MINLEN:25"
what I am doing wrong?. I checked with several examples and my command seems identical to them.