Question: TRIMMOMATRIC Nextera trimming
1
gravatar for meekadi
4.1 years ago by
meekadi10
South Africa
meekadi10 wrote:

Hi, can anyone help? i started using trimmomatic 0.33 today so I'm not that familiar with it. i have paired end data and after checking the quality of my reads i tried trimming for the adapters and low quality using trimmomatic. the adapters used for the my sequences are nextera. i followed the example that was used online for trimming trueseq adapters on an ngs and after trimming the adapters were still detected in my sequences. this is the command i used for my run: java -phred trimmomatic-0.33.jar PE -phred 33 TW_R1.fastq.gz TW_R2.fastq.gz TW_R1trimmed.fastq.gz TW_R2trimmed.fastq.gz ILLUMINACLIP:NexteraPE-PE.fa:2:30:10: LEADING: 3 SLIDINGWINDOW:4:15 MINLEN:40.  

next-gen • 7.1k views
ADD COMMENTlink modified 4.0 years ago by Biostar ♦♦ 20 • written 4.1 years ago by meekadi10
1

Could this help: http://sites.psu.edu/biomonika/2015/07/03/trim-now-or-never-pe-and-mp-adaptor-removal/ (disclaimer: points to my own blog)

ADD REPLYlink written 4.1 years ago by Biomonika (Noolean)3.1k

Thanks Noolean. i read the script. Will try and see which one works for me

ADD REPLYlink written 4.1 years ago by meekadi10

You also need to specify output files for orphan reads (read from a read-pair where the other read got removed). Otherwise the command looks good to me. You should compare the quality profile of fastq files before and after trimming. After you are done with trimming, you can use FastQC to make sure if the adaptors have been removed completely otherwise they will show as over represented sequences in your fastq files. You can also check the quality of reads etc. 

ADD REPLYlink written 4.1 years ago by Ashutosh Pandey11k

Thank you. i trimmed my data again adding what you recommended. i then compared my sequences before and after trimming using fastqc and there is still no  adapters in the trimmed reads but the content  decreased. I'm wondering if it has anything to do with the base position.

ADD REPLYlink written 4.1 years ago by meekadi10
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