Hi,
I'm just wondering how trimming with a sliding window, with a tool such as Trimmomatic, will affect alignment.
If Trimmomatic cuts sequences in the middle of the reads, will that not negatively affect the quality of the alignment, rather than improve it?
An aligner, such as Bowtie2, would not be aware of the missing bases in the middle of the read.
Here is an example of a trimming command from the Trimmomatic website with the sliding window parameter.
java -jar trimmomatic-0.27.jar PE s_1_1_sequence.txt.gz s_1_2_sequence.txt.gz lane1_forward_paired.fq.gz lane1_forward_unpaired.fq.gz lane1_reverse_paired.fq.gz lane1_reverse_unpaired.fq.gz ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Scan the read with a 4-base wide sliding window, cutting when the average quality per base drops below 15
I don't understand how an aligner such as Bowtie2 can generate a better alignment with missing bases in the middle of the reads, rather than keeping the reads, knowing that they are of lesser quality, in the middle of the reads.
Of course, if the trimming reduces the length of the reads below 36, the reads are dropped, which is fine. I am talking about the cases where the entire read is not dropped.
Thank you.
I'm just wondering how trimming with a sliding window, with a tool such as Trimmomatic, will affect alignment.
If Trimmomatic cuts sequences in the middle of the reads, will that not negatively affect the quality of the alignment, rather than improve it?
An aligner, such as Bowtie2, would not be aware of the missing bases in the middle of the read.
Here is an example of a trimming command from the Trimmomatic website with the sliding window parameter.
java -jar trimmomatic-0.27.jar PE s_1_1_sequence.txt.gz s_1_2_sequence.txt.gz lane1_forward_paired.fq.gz lane1_forward_unpaired.fq.gz lane1_reverse_paired.fq.gz lane1_reverse_unpaired.fq.gz ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Scan the read with a 4-base wide sliding window, cutting when the average quality per base drops below 15
I don't understand how an aligner such as Bowtie2 can generate a better alignment with missing bases in the middle of the reads, rather than keeping the reads, knowing that they are of lesser quality, in the middle of the reads.
Of course, if the trimming reduces the length of the reads below 36, the reads are dropped, which is fine. I am talking about the cases where the entire read is not dropped.
Thank you.
Comment