Question: Trimming adaptors with trimmomatic
0
gravatar for Rimma
5 weeks ago by
Rimma20
Hebrew University of Jerusalem
Rimma20 wrote:

I checked my reads with fastQC and found an overrepresentation of Illumina adpaters: https://ibb.co/ftDW6sK enter image description here So I trimmed it using trimmomatic and following command (75 bases Single end reads):

java -jar <path>trimmomatic-0.39.jar SE input.fastq output.fastq ILLUMINACLIP:TruSeq2-SE:2:30:10

and the same with TruSeq3 adapters:

java -jar <path>trimmomatic-0.39.jar SE input.fastq output.fastq ILLUMINACLIP:TruSeq3-SE:2:30:10

However, the output I'm getting is always the same:

Input Reads: 48046117 Surviving: 48046117 (100.00%) Dropped: 0 (0.00%)    
TrimmomaticSE: Completed successfully
  

I'm new to bioinformatics so could you please tell me if there is smth I'm missing why trimmomatic doesn't cut off any of the reads?

rna-seq trimming • 106 views
ADD COMMENTlink modified 5 weeks ago by h.mon27k • written 5 weeks ago by Rimma20

Have the reads been trimmed/ cleaned before, or was this the first time?

Did you run fastqc after to see if the adapters were removed?

ADD REPLYlink written 5 weeks ago by frolic_fern0

I took these files from SRA so I don't know if they were trimmed before. Yes, I checked it looks the same as before trimming...

ADD REPLYlink written 5 weeks ago by Rimma20

It may have to do with the CROP and MINLEN parameters. How long are your reads?

ADD REPLYlink written 5 weeks ago by Hussain Ather940

They are 75 bases long, the same before and after trimming

ADD REPLYlink written 5 weeks ago by Rimma20

The adaptors from illumina have different sequences depending on the version of the kit used for the library preparation. It is possible you are just trimming the wrong sequence. As they have mentioned before, check out the "overrepresented sequences" found at the bottom of the FastQC report and you will know the version of the kit used. Then check for the right sequences and include them in the "TruSeq3-SE" you are using. And include a minim length to drop the reads that are too short after trimming. It should fix your problem.

ADD REPLYlink written 4 weeks ago by jperezboza10
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