Question: Number of reads per lane
0
gravatar for kamel
19 months ago by
kamel30
kamel30 wrote:

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

ADD COMMENTlink modified 19 months ago by genomax84k • written 19 months ago by kamel30
4
gravatar for genomax
19 months ago by
genomax84k
United States
genomax84k wrote:

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.

ADD COMMENTlink modified 19 months ago • written 19 months ago by genomax84k

Thank you genomax for this explanation.

ADD REPLYlink written 19 months ago by kamel30
2
gravatar for grant.hovhannisyan
19 months ago by
grant.hovhannisyan2.0k wrote:

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.

ADD COMMENTlink modified 19 months ago • written 19 months ago by grant.hovhannisyan2.0k

Thank you now it's very clear

ADD REPLYlink written 19 months ago by kamel30
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