Question: Base pair order in sequencer vs in fastq
0
gravatar for DVA
9 months ago by
DVA480
United States
DVA480 wrote:

For illumina platform, after the reads bind to the chip and bridge amplified, machine reads each read from top to bottom. I am wondering how does this top-bottom order transfer to fastq files. Does it become left to right? In anther word, (assuming index sequence shows in the naming line of fastq, not with the read.) the adaptor that is close to the bottom of chip, will be at the right end of each read (assume this adaptor gets sequenced).

Thank you very much.

sequencing • 1.4k views
ADD COMMENTlink modified 9 months ago by finswimmer8.1k • written 9 months ago by DVA480
4
gravatar for finswimmer
9 months ago by
finswimmer8.1k
Germany
finswimmer8.1k wrote:

Hello DVA,

yes, "top-to-bottom" becomes "left-to-right". The sequencing direction is always 5' to 3' and that's what you have also in your fastq files. You can also say, the first base you sequence is also the first base in your fastq file.

Here is also a nice picture about the sequence process.

fin swimmer

ADD COMMENTlink written 9 months ago by finswimmer8.1k

Thank you for the confirmation!

ADD REPLYlink written 9 months ago by DVA480
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