[lorendarith]

33,676,040 raw reads
8,452,686,040 raw bases
251 length

33,156,566 reads after adapter and quality trimming
7,559,421,635 bases after trimming
30-251 length with a mean of 227
1% of the sequences lost to trimming
10% of the bases lost to trimming

What was the quality trimming exactly?

[matth431]

Just got 10.3Gbp raw data, histogram suggested 7.0Gbp >Q30 by end of 251|6|251 run. Useable sequence (post-QC trim) checking it on Genomics Workbench probably closer to 9Gbp. About 39.5M reads with average length of 225bp.

Cluster density of 1300K/mm2 - same library gave ~3.5Gbp on a v1 flowcell with 2x151bp reads (clustered at 8pM).

[Shimul]

Hi All,

I am finally running of my bacterial pooled DNA library (which I made using Nextera XT) on the Miseq using MiSeq V3. I have checked the machine now and it shows that after 70 cycles, the >=Q30 is 96%, cluster passing filter 91.4%, and the cluster density is 1092K/mm.

Do you think that the run is going well?

Hope to hear back from you soon again!

Cheers,

Shimul

[pmiguel]

Hi All,

I am finally running of my bacterial pooled DNA library (which I made using Nextera XT) on the Miseq using MiSeq V3. I have checked the machine now and it shows that after 70 cycles, the >=Q30 is 96%, cluster passing filter 91.4%, and the cluster density is 1092K/mm.

Do you think that the run is going well?

Hope to hear back from you soon again!

Cheers,

Shimul

Sure, those metrics would consistent with the start of a good run.

--
Phillip

[Shimul]

Sure, those metrics would consistent with the start of a good run.

--
Phillip

The Q30 is now 83.1% after 250 cycles, yesterday it was 96% after 70 cycles. But rest of the parameters are consistent: clusters PF 91.4%, cluster density 1092K/mm^2, which are the same as yesterday. Do you speculate anything? DO you think that the run will be okay?

Many thanks.

Shimul

[GenoMax]

The Q30 is now 83.1% after 250 cycles, yesterday it was 96% after 70 cycles. But rest of the parameters are consistent: clusters PF 91.4%, cluster density 1092K/mm^2, which are the same as yesterday. Do you speculate anything? DO you think that the run will be okay?

Many thanks.

Shimul

Sounds like this is your first ever run and you are anxious

Cluster density does not change over the run duration. As @nucacidhunter pointed out Q scores may keep dropping. Enjoy the weekend and don't worry about the run.

[kmcarr]

Sounds like this is your first ever run and you are anxious

Cluster density does not change over the run duration. As @nucacidhunter pointed out the PF% will likely continue dropping as will the Q scores. Enjoy the weekend and don't worry about the run.

A correction Geno, %PF does not change. PF clusters are set at cycle 25. Q scores of course are calculsted on each cycle and later cycles always have lower quality than earlier ones.

Shimul, relax, your run is going fine.

[nucacidhunter]

Sounds like this is your first ever run and you are anxious

Cluster density does not change over the run duration. As @nucacidhunter pointed out the PF% will likely continue dropping as will the Q scores. Enjoy the weekend and don't worry about the run.

I think it is less accurate quote of my post (#65) from the following:

http://seqanswers.com/forums/showthr...738#post202738

[GenoMax]

I think it is less accurate quote of my post (#65) from the following:

http://seqanswers.com/forums/showthr...738#post202738

@nucacidhunter: Please accept my apologies. Thank you @kmcarr also. I should have checked my post more carefully (I have made necessary correction above).