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Search: Posts Made By: Jessica_L
Forum: Illumina/Solexa 08-10-2017, 07:26 AM
Replies: 9
Views: 1,735
Posted By Jessica_L
Technically, yes, but whether you would want to...

Technically, yes, but whether you would want to do so will depend partially on your coverage needs and your tolerance for sequencing errors.

Using paired end reads of 300bp from either end will...
Forum: Illumina/Solexa 08-07-2017, 01:32 PM
Replies: 1
Views: 1,054
Posted By Jessica_L
Hi Maria, I'm not familiar with this exact...

Hi Maria,

I'm not familiar with this exact error message but it sounds like the machine may have had difficulty finding a plane of focus for the flow cell.

The very first thing you should do...
Forum: Illumina/Solexa 07-21-2017, 07:30 AM
Replies: 22
Views: 3,989
Posted By Jessica_L
No problem! Keep us posted on your progress and...

No problem! Keep us posted on your progress and let us know if you need any more help.
Forum: Illumina/Solexa 07-20-2017, 12:21 PM
Replies: 22
Views: 3,989
Posted By Jessica_L
It looks to me like you might be having two...

It looks to me like you might be having two problems, though the degree to which each contributes to a failed run may be hard to isolate

The 16s libraries seem to be causing an issue since they're...
Forum: Illumina/Solexa 07-20-2017, 09:50 AM
Replies: 22
Views: 3,989
Posted By Jessica_L
I'm not sure. The change in PhiX might be the...

I'm not sure. The change in PhiX might be the issue-- this does seem to be pretty low diversity sequence, but I can't imagine that 15% instead of 20% could make that much of a difference.

I'm a...
Forum: Illumina/Solexa 07-20-2017, 07:47 AM
Replies: 22
Views: 3,989
Posted By Jessica_L
I noticed the phasing/prephasing numbers, too,...

I noticed the phasing/prephasing numbers, too, Joe, but when compared to test 16s data from Illumina on basespace, the data here really don't seem all that extreme.

Joanna-- you said you quantify...
Forum: Illumina/Solexa 07-19-2017, 08:33 AM
Replies: 22
Views: 3,989
Posted By Jessica_L
Also, can you post some screenshots of the run...

Also, can you post some screenshots of the run metrics: the run and lane metrics table, an intensity vs cycle plot (the charts dashboard page from basespace is perfect), and maybe a screenshot of one...
Forum: Illumina/Solexa 07-19-2017, 08:28 AM
Replies: 22
Views: 3,989
Posted By Jessica_L
If the sequencer appears to be working correctly...

If the sequencer appears to be working correctly and you've ruled out any issues with the primers, I think the library is the next best area to troubleshoot.

You mentioned you made new primer...
Forum: Illumina/Solexa 05-31-2017, 09:08 AM
Replies: 1
Views: 759
Posted By Jessica_L
if you have 1000ul of library at 15pM, you should...

if you have 1000ul of library at 15pM, you should have 15000pmol of material. 25% of that should be 3750pmol (that'll be your PhiX target). There are three ways to proceed:
From the 20pM denatured...
Forum: Illumina/Solexa 01-19-2017, 08:40 AM
Replies: 68
Views: 19,982
Posted By Jessica_L
My lab is looking at bringing in the TruSight...

My lab is looking at bringing in the TruSight Tumor 15 assay. It seems like most of the v3 issues are related to low complexity libraries (16s RNA-seq reads, etc.) so I'm assuming that we'll be okay...
Forum: Illumina/Solexa 01-11-2017, 08:36 AM
Replies: 113
Views: 24,742
Posted By Jessica_L
Thanks for the info and updates, kmcarr. I...

Thanks for the info and updates, kmcarr. I haven't had a chance to see a NextSeq in action so I didn't realize all the channels loaded from a single input.
Forum: Illumina/Solexa 01-10-2017, 09:44 AM
Replies: 113
Views: 24,742
Posted By Jessica_L
It's hard to say. The HiSeq 3000/4000 sheet list...

It's hard to say. The HiSeq 3000/4000 sheet list the following:
532 nm, 660 nm, 650 nm (barcode reader)
MiSeq uses the 530 nm, 660 nm, too.

The NextSeq sheet has
520 nm, 650 nm; Laser diode:...
Forum: Illumina/Solexa 01-10-2017, 09:39 AM
Replies: 113
Views: 24,742
Posted By Jessica_L
That was going to be my next question. For...

That was going to be my next question.

For the question regarding flow cell lanes, here's a screencap from the Illumina website. The flow cells definitely have lanes, albeit fewer than the 8...
Forum: Illumina/Solexa 01-10-2017, 09:23 AM
Replies: 113
Views: 24,742
Posted By Jessica_L
Where did you see that it's two color? The spec...

Where did you see that it's two color? The spec sheet lists four different laser wavelengths (532, 660, 780, 790nm), so I was hopeful they were going back to that.
Forum: Illumina/Solexa 10-17-2016, 09:30 AM
Replies: 18
Views: 5,747
Posted By Jessica_L
Hi dorix, The issue you're having is, I...

Hi dorix,

The issue you're having is, I think, rather common. It helps to look at the overall shape of the electropherogram in the bioanalyzer data and make sure that it looks like appropriate for...
Forum: Illumina/Solexa 09-27-2016, 01:41 PM
Replies: 28
Views: 3,505
Posted By Jessica_L
That's good to know, thermophile, thanks. I'm...

That's good to know, thermophile, thanks. I'm probably going to have to ask for that $5k to be added into our budget for next year.
Forum: Illumina/Solexa 09-27-2016, 10:40 AM
Replies: 28
Views: 3,505
Posted By Jessica_L
That's kind of what I'm wondering, too, GenoMax?...

That's kind of what I'm wondering, too, GenoMax? We have a pretty small operation, but I do also send out for larger jobs and I still need to analyze data sometimes.
Forum: Illumina/Solexa 09-27-2016, 09:01 AM
Replies: 28
Views: 3,505
Posted By Jessica_L
Wait, so we can't even do FastQC with a free...

Wait, so we can't even do FastQC with a free account? I was able to run it, but like I said yesterday, my account is still in trial mode. Are you just trying to use the Illumina/BaseSpace Labs 16s...
Forum: Illumina/Solexa 09-26-2016, 11:16 AM
Replies: 28
Views: 3,505
Posted By Jessica_L
Does that apply to all apps or just the third...

Does that apply to all apps or just the third party ones that we would normally be paying for? Right now, it looks like the usual basic analyses I'm used to running are still accessible from a basic...
Forum: Illumina/Solexa 08-31-2016, 07:06 AM
Replies: 6
Views: 2,015
Posted By Jessica_L
Your best bet on that score is probably your...

Your best bet on that score is probably your field support from Illumina, for a MiSeq probably your FAS. The error codes aren't closely guarded secrets, but I'm not aware of a collection of codes...
Forum: Illumina/Solexa 08-25-2016, 10:12 AM
Replies: 6
Views: 2,015
Posted By Jessica_L
What Genomax said. I'd add that if you...

What Genomax said.

I'd add that if you don't have your MiSeq under a maintenance agreement, you may want to consider getting one first, as the service visit and repair can easily exceed the cost...
Forum: Illumina/Solexa 08-10-2016, 05:49 AM
Replies: 2
Views: 1,862
Posted By Jessica_L
The HiSeq 4000 has its own set of cluster kits...

The HiSeq 4000 has its own set of cluster kits and sequencing reagents, from what I can tell. See page 2 here for run specs: ...
Forum: Illumina/Solexa 08-01-2016, 10:26 AM
Replies: 6
Views: 1,153
Posted By Jessica_L
In theory, I think you might be okay to use the...

In theory, I think you might be okay to use the 20pM denatured libraries? 20pM PhiX is good for something like three weeks, but I'd add a caveat about not assuming they'll just behave the same. Like...
Forum: Illumina/Solexa 07-12-2016, 08:00 AM
Replies: 1
Views: 854
Posted By Jessica_L
I think you might be okay? If possible, a...

I think you might be okay? If possible, a bioanalyzer run on the completed libraries could help you figure out if there are improperly formed products and if the size of the main insert/library is...
Forum: Illumina/Solexa 07-06-2016, 11:19 AM
Replies: 23
Views: 4,074
Posted By Jessica_L
That's a good point, GenoMax-- for the TruSeq...

That's a good point, GenoMax-- for the TruSeq Amplicon v1 that I've used, the library that's eluted off beads post-normalization is single stranded in dilute NaOH and that requires a short heating...
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