I have a very basic question.
How does the machine know a read belongs to a certain index?
let's say we have a sequence like this in a single end RNA-Seq:
5' end adapter-cDNA-index-3' end adapter
For each read, sequencing starts from 5' end and ends a certain place with cDNA because the fragment of 5' end adapter-cDNA-index-3' end adapter is longer than the reads.
Apparently, the index is not contained the reads.
So how does the machine know a read belongs to a certain index?
How does the machine know a read belongs to a certain index?
let's say we have a sequence like this in a single end RNA-Seq:
5' end adapter-cDNA-index-3' end adapter
For each read, sequencing starts from 5' end and ends a certain place with cDNA because the fragment of 5' end adapter-cDNA-index-3' end adapter is longer than the reads.
Apparently, the index is not contained the reads.
So how does the machine know a read belongs to a certain index?
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