running trimmomatic inside Trinity

Question

[lay_0]

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.

Thanks!

[GenoMax]

From Trinity wiki

[> --quality_trimming_params <string> defaults to: \ #

"ILLUMINACLIP:$TRIMMOMATIC_DIR/adapters/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:5 LEADING:5 TRAILING:5 MINLEN:25"]

If you want to change parameters follow the command structure above.
Explanation for trimmomatic parameters is here.

[lay_0]

thanks, I don't know how that is different from what I did. Using the ILLUMINACLIP and SLIDINGWINDOWS options doesn't change anything, it still give me the same error.

[GenoMax]

It appears that you have forgotten to include --trimmomatic option in your trinity command to indicate to trinity that you want to run that program.

[lay_0]

I did run with the --trimmomatic option in the beginning and it didn't work, trying things I deleted it.

[GenoMax]

Can you try with following options? Replace $TRIMMOMATIC_DIR with real path to the adapters file on your system.

--trimmomatic --quality_trimming_params "ILLUMINACLIP:$TRIMMOMATIC_DIR/adapters/TruSeq3-PE.fa:2:30:10 TRAILING:2 MINLEN:25"

[lay_0]

Thank you so much for your help @genomax2. I did tried that, I don't really need ILLUMINACLIP option because I don't want to use it, my reads were trimmed for adapters at the sequencing center, but seeing that wiring only the two other options wasn't working, I tried writing the command exactly like in most examples out there (with the ILLUMINACLIP option), and yes, I made sure the path to adapters was correct. Didn't work. I decided to run trimmomatic outside trinity and it worked fine, now I am running the assembly, still not knowing what was wrong.

[GenoMax]

I guess we won't know what the problem was then .. but as long as you got it to work.