Number of reads per lane

Question

[kamel]

Hi Biostar,

Apologies for this basic question but I can not find a simple answer

I want to sequence several samples of mRNA paired end 2x150 and for each sample I want 100 million reads (100 million for forward and 100 million for reverse)

the supplier proposes to sequence 3 samples per lane of flow cell of the Hiseq 4000 technology. So what I understood 3 samples x 200 million reads (100 million for forward and 100 million for reverse) = 600 million reads per lane

but when I looked for the performances Illumina Hiseq 4000 I found this technology can generate 312000000 Clusters per lane only. How can this technology generate 600 million reads per lane ??

Would it be possible to give me a simple answer Thank you in advance

Answer 1

[GenoMax]

Illumina traditionally counts two reads coming from a single cluster independently. 312000000 passing clusters give rise to 312000000 x 2 = Number of reads per lane.

Please keep in mind this number if attainable with excellent quality genomic DNA libraries. Any deviation from this will result in lower yields.

[kamel]

Thank you genomax for this explanation.

Answer 2

[grant.hovhannisyan]

What is sequenced is a so called "fragment". To simplify, they will sequence each sample with 100 mln fragments, and each fragment is sequenced from both ends, i.e. paired end sequencing. And for each fragment you will have two reads - forward and reverse. So what the provider tells you is correct. Anyway, always ask them for details and explanations if you have doubts to avoid potential misunderstandings and waste of resources.

[kamel]

Thank you now it's very clear