Dear all,
I have few questions about the trimming of adapters with Trimmomatic. I have 2x150 bp paired end runs from Illumina MiSeq system. Normally, based on FastQC, there should not be a lot of remaining adapters on the sequencing results (not detected as overrepresented sequences) . However, I think it should be better to use Trimmomatic to trimm the remaining adapters. But I am not sure to really understand how it works. If I understand well, for paired-end reads, it will simulate an adapter at the end of each forward and reverse reads based on the fasta file supplied, and then hybridize the two reads by their common features (i.e, the nucleotides corresponding to the sequenced gene). If the adapter of one read have alignment on the other one, it will be trimmed on the read. Is it true?
My problem is for the keepBothReads option. I don't understand when I should use it. At the end of the trimming and quality filtering, I would like to get two files, one for forward and one for reverse, to do the alignment with Bowtie 2. In addition, I tried Trimmomatic with and without keepBothReads option and this gave me different results: I had trimmed reads for the forward sequences without keepBothReads (around 16%), however, there was no more trimmed reads if I used the keepBothReads option. Could anyone just explain me when I should use or not this option?
Here are the command lines I used:
Without keepBothReads:
java -jar ../../../../../soft/Trimmomatic-0.33/trimmomatic-0.33.jar PE 110413_6_JY747_GCCAAT_L001_R1_001.fastq 110413_6_JY747_GCCAAT_L001_R2_001.fastq forward_true_paired.fastq forward_true_unpaired.fastq reverse_true_paired.fastq reverse_true_unpaired.fastq ILLUMINACLIP:../../../../../soft/Trimmomatic-0.33/adapters/TruSeq3-PE.fa:2:30:10
With keepBothReads:
java -jar ../../../../../soft/Trimmomatic-0.33/trimmomatic-0.33.jar PE 110413_6_JY747_GCCAAT_L001_R1_001.fastq 110413_6_JY747_GCCAAT_L001_R2_001.fastq forward_true_paired.fastq forward_true_unpaired.fastq reverse_true_paired.fastq reverse_true_unpaired.fastq ILLUMINACLIP:../../../../../soft/Trimmomatic-0.33/adapters/TruSeq3-PE.fa:2:30:10:8:TRUE
Thank you very much for your help.
Best,
Nicolas
I have few questions about the trimming of adapters with Trimmomatic. I have 2x150 bp paired end runs from Illumina MiSeq system. Normally, based on FastQC, there should not be a lot of remaining adapters on the sequencing results (not detected as overrepresented sequences) . However, I think it should be better to use Trimmomatic to trimm the remaining adapters. But I am not sure to really understand how it works. If I understand well, for paired-end reads, it will simulate an adapter at the end of each forward and reverse reads based on the fasta file supplied, and then hybridize the two reads by their common features (i.e, the nucleotides corresponding to the sequenced gene). If the adapter of one read have alignment on the other one, it will be trimmed on the read. Is it true?
My problem is for the keepBothReads option. I don't understand when I should use it. At the end of the trimming and quality filtering, I would like to get two files, one for forward and one for reverse, to do the alignment with Bowtie 2. In addition, I tried Trimmomatic with and without keepBothReads option and this gave me different results: I had trimmed reads for the forward sequences without keepBothReads (around 16%), however, there was no more trimmed reads if I used the keepBothReads option. Could anyone just explain me when I should use or not this option?
Here are the command lines I used:
Without keepBothReads:
java -jar ../../../../../soft/Trimmomatic-0.33/trimmomatic-0.33.jar PE 110413_6_JY747_GCCAAT_L001_R1_001.fastq 110413_6_JY747_GCCAAT_L001_R2_001.fastq forward_true_paired.fastq forward_true_unpaired.fastq reverse_true_paired.fastq reverse_true_unpaired.fastq ILLUMINACLIP:../../../../../soft/Trimmomatic-0.33/adapters/TruSeq3-PE.fa:2:30:10
With keepBothReads:
java -jar ../../../../../soft/Trimmomatic-0.33/trimmomatic-0.33.jar PE 110413_6_JY747_GCCAAT_L001_R1_001.fastq 110413_6_JY747_GCCAAT_L001_R2_001.fastq forward_true_paired.fastq forward_true_unpaired.fastq reverse_true_paired.fastq reverse_true_unpaired.fastq ILLUMINACLIP:../../../../../soft/Trimmomatic-0.33/adapters/TruSeq3-PE.fa:2:30:10:8:TRUE
Thank you very much for your help.
Best,
Nicolas
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