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4.8 years ago
vishalchanda364
▴
20
Hello, I was trimming my metagnomic data which is illumina paired end sequences using trimmomatic-0.36 but the results are not satisfying. the command which I am running is: java -jar trimmomatic-0.36 PE -phred33 <file1.fq> <file2.fq> ILLUMINACLIP:TruSeq3-PE-2.fa\:2\:30\:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Can anyone help me out with the command as I am not sure about the adapter removal part in the same?
Results need to be scientifically correct. Is something not working to make them so?
Yes.! The results obtained are not satisfying, the QC of the results is much worse than the raw data.
Please show us in what way. FastQC plots?
In your Trimmomatic command, not sure why you escaped the colons in the ILLUMINACLIP bit (\:2\:30\:10) but not the other colons? Also, Trimmomatic is very fussy about the format of the sequence names in the .fa file so it would help to add the relevant part of that file to your question. By 'metagenomics' do you mean 16S profiling? What QC are you applying?
I've made a tool for visualizing trimming results which you may find handy to verify that the trimming is proceeding as you expect and whether there are residual adapter sequences (I've run into the same problem as you and got sick of poring over pre-trimmed and post-trimmed fastq files manually!) It's here: https://github.com/MonashBioinformaticsPlatform/trimviz.git
Dependencies are in the help menu (python2 trimviz.py -h). Sorry I haven't got around to containerizing it yet - you'll need seqtk plus a few python and R libraries installed.