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Search: Posts Made By: sfranzenburg
Forum: General 05-23-2017, 06:18 AM
Replies: 2
Views: 1,303
Posted By sfranzenburg
I just need once single strain to establish and...

I just need once single strain to establish and assess performance of the MinION in our lab.
I think I will just go for e.coli K12.
Just figured I'd ask if there is any gold standard.
Forum: General 05-22-2017, 05:30 AM
Replies: 2
Views: 1,303
Posted By sfranzenburg
Bacterial Genome in a Bottle

Dear All,

I am searching for the bacterial equivalent of the human "Genome in a Bottle", meaning a commercially available bacterial reference DNA to assess Sequencing Performance.
Is there such a...
Forum: Sample Prep / Library Generation 05-15-2017, 09:59 PM
Replies: 5
Views: 1,392
Posted By sfranzenburg
Thank you all, Meyer protocol seems to be...

Thank you all,
Meyer protocol seems to be exactly what we were searching for.
Forum: Sample Prep / Library Generation 05-08-2017, 06:03 AM
Replies: 5
Views: 1,392
Posted By sfranzenburg
Reverse Engineering of Primer mix by NGS

Dear All,

we have a primer mix of unknown sequences. Has anyone tried yet to create NGS libraries with this primer mix as templates to reverse engineer their sequence?
At first we thought about...
Forum: Sample Prep / Library Generation 09-18-2015, 05:06 AM
Replies: 4
Views: 3,407
Posted By sfranzenburg
That is what you will get from your facility. ...

That is what you will get from your facility.
They will run the illumina bcl2fastq script and you will get a fastq file for each sample individually (or 2 if you do paired end sequencing).

Good...
Forum: Sample Prep / Library Generation 09-18-2015, 04:54 AM
Replies: 4
Views: 3,407
Posted By sfranzenburg
Hi Matt, as long as your index strategy...

Hi Matt,

as long as your index strategy allows it, pooling all samples is absolutely fine and the way to go for your problem. So, as long as all your samples have different indices (or a different...
Forum: Illumina/Solexa 08-24-2015, 05:14 AM
Replies: 2
Views: 2,402
Posted By sfranzenburg
Thanks a lot. That really helps keeping the...

Thanks a lot. That really helps keeping the amount of toxic waste in check. The formamid-containing waste of the HiSeq and cBot is enough. HiSeq X-Ten labs must drown in that stuff...
Forum: Illumina/Solexa 08-17-2015, 01:35 AM
Replies: 2
Views: 2,402
Posted By sfranzenburg
ProClin-Waste: What do you do with it?

Hi,
how do you discard your HiSeq 3000/4000 "Maintenance Wash Solution", containing ProClin? According to the MSDS, this compound is quite a nasty one.
It makes up 0,0003% of the wash solution, but...
Forum: Bioinformatics 06-03-2015, 05:57 AM
Replies: 4
Views: 2,153
Posted By sfranzenburg
Hi fibar, first, thank you very much for your...

Hi fibar,
first, thank you very much for your answer, it helps.

It is just frustrating to see publications claiming two microbiotas are different based on PCA of MG-RAST data, which still include...
Forum: Illumina/Solexa 02-23-2015, 10:55 PM
Replies: 5
Views: 4,009
Posted By sfranzenburg
I did it and "re-activated" the beads with...

I did it and "re-activated" the beads with self-made PEG buffer. Worked really well.
Forum: Sample Prep / Library Generation 01-13-2015, 05:27 AM
Replies: 7
Views: 5,972
Posted By sfranzenburg
Hi, I basically tried exactly that with gut...

Hi,
I basically tried exactly that with gut bacteria from Insects.
I pulled euk. mRNA with Poly A and removed euk. and prok. rRNA with the Ribozero Kits.
The result was disappointing, as still a...
Forum: Sample Prep / Library Generation 12-18-2014, 09:25 PM
Replies: 2
Views: 1,018
Posted By sfranzenburg
Well, that was my understanding as well. But...

Well, that was my understanding as well.
But the fact that the Quantifluor-Manual states that you should use standards of the same size as the sample made me wonder if it is really linear.

quote...
Forum: Sample Prep / Library Generation 12-18-2014, 04:24 AM
Replies: 2
Views: 1,018
Posted By sfranzenburg
Library Quantification - Size Adjustment

Hi,
when you measure the concentration of your input gDNA or libraries (illumina nextera in my case), do you use the same DNA standards (=kit contents) for both? In my understanding, the standards...
Forum: Ion Torrent 12-16-2014, 04:45 AM
Replies: 2
Views: 1,761
Posted By sfranzenburg
Are you sure this command is still valid? ...

Are you sure this command is still valid?
Usually, the Qiime OTU tables are in .biom file format since ~2 years.
Forum: Illumina/Solexa 12-04-2014, 01:52 AM
Replies: 0
Views: 1,253
Posted By sfranzenburg
Basespace and Run-Summary questions

Hi,
I am preparing for my first Nextseq run, so I am exploring Basespace.

I made up "test-samples" to just learn the process of setting up a run from biological sample input, to libraries, pools...
Forum: Sample Prep / Library Generation 12-03-2014, 11:32 PM
Replies: 0
Views: 1,446
Posted By sfranzenburg
Exome Sequencing on NextSeq500

We are planning to run human exomes on Illumina's Nextseq and I just wanted to confirm that I got some details right.

We will use the TruSight One and Rapid Capture Kits and I have a small...
Forum: Illumina/Solexa 11-17-2014, 05:12 AM
Replies: 2
Views: 1,325
Posted By sfranzenburg
Thank you, the info that their estimates are...

Thank you,
the info that their estimates are conservative is already important for me. Naively I thought these are very optimistic.
Forum: Illumina/Solexa 11-17-2014, 04:59 AM
Replies: 2
Views: 1,325
Posted By sfranzenburg
Exome Sequencing on NextSeq500

Hi,
our lab is currently sequencing human exomes on Ion Proton Sequencers.
Now, we plan to give the NextSeq500 a try (first steps into the Illumina world).

We plan on using the Rapid Capture...
Forum: Bioinformatics 04-16-2014, 10:47 AM
Replies: 0
Views: 1,089
Posted By sfranzenburg
Metagenome Comparisons in MG-RAST

Hi,

Often, I see that authors compare different metagenomes from MG-RAST and finally conclude that "Pathway X" is stronger represented in the microbial community A than in community B.

However,...
Forum: Bioinformatics 04-10-2014, 07:28 AM
Replies: 4
Views: 2,153
Posted By sfranzenburg
No one? How can you compare two different...

No one?

How can you compare two different samples of host-associated metagenomes when they contain a huge amount of host reads? Of course they will be different, of course they cluster by...
Forum: Bioinformatics 04-08-2014, 09:58 AM
Replies: 4
Views: 2,153
Posted By sfranzenburg
Mg-rast api

Hi,

I have uploaded my metagenome files to MG-RAST. 30% of my reads are bacterial, which is what I expected.

How can I extract all bacterial reads only? I want to perform all my downstream...
Forum: Bioinformatics 03-26-2014, 05:07 AM
Replies: 9
Views: 1,912
Posted By sfranzenburg
Ok, thanks alot Brian. Than I will the discard...

Ok, thanks alot Brian.
Than I will the discard the reads.
I read some papers for MDA before I did it and I don't recall that they brought up this problem.
Forum: Bioinformatics 03-25-2014, 04:37 PM
Replies: 9
Views: 1,912
Posted By sfranzenburg
Hi Brian, thanks alot. I did MDA for 8h to...

Hi Brian,
thanks alot.
I did MDA for 8h to amplify my original DNA (library prep protocol wanted to have 1 g, which was far more than I had). Library Prep was basically the same as with the...
Forum: Bioinformatics 03-25-2014, 12:28 PM
Replies: 9
Views: 1,912
Posted By sfranzenburg
Thanks. I meanwhile found my lost reads. Most...

Thanks.
I meanwhile found my lost reads. Most of them were removed in MG-RASTs dereplication step (50% removed). Is dereplication state of the art for Illumina data today? 50% loss sound very high...
Forum: Bioinformatics 03-25-2014, 10:57 AM
Replies: 9
Views: 1,912
Posted By sfranzenburg
Just got a reply from the MG-RAST support (didn't...

Just got a reply from the MG-RAST support (didn't expect them to react that fast, thats why I got here for help too). Seems like I have misinterpreted their numbers.
When I saw average ambig chars:...
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