running trimmomatic inside Trinity
0
0
Entering edit mode
8.6 years ago
lay_0 ▴ 50

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!

Assembly Trinity RNA-seq trimmomatic • 6.5k views
ADD COMMENT
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

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.

ADD REPLY
1
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

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

ADD REPLY
2
Entering edit mode

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"
ADD REPLY
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 1292 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6