Question: Trimmomatic trimming principle
0
gravatar for shuchen
2.0 years ago by
shuchen10
shuchen10 wrote:

Why the whole read has to be clipped when the technical sequence overlap or partial overlap with the 5' end of the read?

Figure 1 illustrates the alignments tested for each technical sequence. The process begins with a partial overlap of the 3′ end of the technical sequence with the 5′ end of the read, as shown in (A). Testing proceeds by moving the putative contaminant toward the 3′ end of the read. In both the partial overlap (A) and complete overlap at the 5′ end (B) scenarios, the entire read will be clipped. If the contaminant is found within the read (C), the bases from the 5′ end of the read to the beginning of the alignment are retained. The testing process continues until only a partial alignment on the 3′ end of the read remains (D).

Figure 1 illustrates the alignments tested for each technical sequence. The process begins with a partial overlap of the 3′ end of the technical sequence with the 5′ end of the read, as shown in (A). Testing proceeds by moving the putative contaminant toward the 3′ end of the read. In both the partial overlap (A) and complete overlap at the 5′ end (B) scenarios, the entire read will be clipped. If the contaminant is found within the read (C), the bases from the 5′ end of the read to the beginning of the alignment are retained. The testing process continues until only a partial alignment on the 3′ end of the read remains (D).

read trimming trimmomatic • 631 views
ADD COMMENTlink modified 2.0 years ago • written 2.0 years ago by shuchen10

I am unsure what you mean but if a part of the read is recognized as adapter, any sequence that follows must be part of the sequencing adapter and therefore be removed.

ADD REPLYlink written 2.0 years ago by Gabriel R.2.6k

I meant why not only clip off the 5' end that was recognized as adapter sequence and retain the rest of read?

ADD REPLYlink written 2.0 years ago by shuchen10

You keep the sequence "left" of it (left=before 5' end of the adapter sequence) but the following should just be the remainder adapter sequence.

ADD REPLYlink written 2.0 years ago by Gabriel R.2.6k

Thank you very much for your reply. This is exactly where I got confused. Why the following will be the remainder adapter sequence? Is it possible that a read is consist of the 3' end of the adapter sequence and valid sequence as below?

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ADD REPLYlink modified 2.0 years ago • written 2.0 years ago by shuchen10

If the read starts with the adapter sequence, then your insert size is 0 and you had 2 adapters joined together.

ADD REPLYlink written 2.0 years ago by Gabriel R.2.6k
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