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Search took 0.00 seconds. Search: Posts Made By: JasperGeh
Forum: Bioinformatics 02-06-2020, 12:36 AM
Replies: 2
Views: 1,111
Posted By JasperGeh
Yes, I have stumbled upon that but haven't tried...

Yes, I have stumbled upon that but haven't tried it yet. Is that the "gold standard" for human read removal, if there is something like that?
Forum: Bioinformatics 02-04-2020, 06:56 AM
Replies: 2
Views: 1,111
Posted By JasperGeh
Lightbulb Human read filtering with Kraken 2

Hey everyone,

I was wondering something regarding the usage of Kraken 2 for read filtering.
I sequence/assemble viruses and inherited a pipeline in which human reads were removed by a simple...
Forum: Oxford Nanopore 04-05-2019, 04:50 AM
Replies: 2
Views: 4,949
Posted By JasperGeh
ssDNA sequencing on MinION without PCR or doublestranding

Hey people!

A colleague of mine wants to sequence a library of ssDNA Adeno-associated viruses on the MinION to get a distribution of their genome sizes and orientations.
To get the size...
Forum: Illumina/Solexa 04-03-2019, 09:36 AM
Replies: 5
Views: 2,069
Posted By JasperGeh
Not for this, as it's an antibody library and we...

Not for this, as it's an antibody library and we need a single paired read with low error rate to cover one fragment. Hacking it will probably be ;)
Forum: Illumina/Solexa 04-02-2019, 09:02 AM
Replies: 5
Views: 2,069
Posted By JasperGeh
Thanks, what they did in the paper looks really...

Thanks, what they did in the paper looks really cool. And yes, I am aware of the decreasing quality, but a small amount of data (after filtering) helps us more than none, in this case...
Forum: Illumina/Solexa 04-01-2019, 03:07 AM
Replies: 5
Views: 2,069
Posted By JasperGeh
Increasing MiSeq v3 cycle number for >600bp reads

Hello people!

We have a sequencing application where we could really need, say, 50–100 more cycles from a 600-cycle MiSeq v3 kit.

Illumina states that the cartridge contains reagents for 625...
Forum: Oxford Nanopore 03-04-2019, 03:08 AM
Replies: 1
Views: 3,589
Posted By JasperGeh
MinKNOW Version for late-2017 flow cells

Hello people!

My institute bought a MinION starter set with two flow cells in late 2017 and never got around trying it.
Now we have some samples for which we could need the long reads and I'm...
Forum: Illumina/Solexa 02-06-2019, 05:48 AM
Replies: 2
Views: 2,324
Posted By JasperGeh
Yep, that's what I was looking for, thanks....

Yep, that's what I was looking for, thanks. Somehow missed it while searching. Apologies!
Forum: Illumina/Solexa 02-06-2019, 04:20 AM
Replies: 2
Views: 2,324
Posted By JasperGeh
Lightbulb Combining TruSeq and Nextera XT Indices

Hello people,

we usually prepare and run the samples on our MiSeq using the 26 6nt-long i7 TruSeq DNA Indices (formerly TruSeq LT, I think). A colleague want's to add a single sample to one of our...
Forum: Sample Prep / Library Generation 12-17-2018, 02:15 AM
Replies: 4
Views: 2,086
Posted By JasperGeh
Alright, could be it. I assume there are a number...

Alright, could be it. I assume there are a number of online resources on how to avoid dimer formation?

And thanks, I will try a 0.8x cleanup before sequencing.
Forum: Sample Prep / Library Generation 12-14-2018, 04:22 AM
Replies: 4
Views: 2,086
Posted By JasperGeh
ScriptSeq v2 135base-peak

Hello people,

I tried the ScriptSeq v2 RNA Library Prep Kit on the total RNA extract of a cerebrospinal fluid sample. The RNA amount was not measureable with our Qubit but I tried anyway. I...
Forum: Illumina/Solexa 09-25-2018, 11:44 AM
Replies: 7
Views: 1,850
Posted By JasperGeh
It is our own MiSeq and we will have tech support...

It is our own MiSeq and we will have tech support take a look at it. But from first sighting of the reads it actually does look like the short inserts have outcompeted the larger ones during...
Forum: Illumina/Solexa 09-24-2018, 06:33 AM
Replies: 7
Views: 1,850
Posted By JasperGeh
Ah, low diversity between the clusters in each...

Ah, low diversity between the clusters in each sequencing cycle, I understand how that would be problematic.
Yes, it is a V3 run.
And I see how a overclustering of smaller inserts would lead to...
Forum: Illumina/Solexa 09-24-2018, 05:36 AM
Replies: 7
Views: 1,850
Posted By JasperGeh
Thanks for your ideas. 1. In a...

Thanks for your ideas.

1. In a population-genetics sense? And what is the underlying mechanism between the nucleotide diversity and basecall quality? But I guess not; every sample is the complete...
Forum: Illumina/Solexa 09-24-2018, 02:25 AM
Replies: 7
Views: 1,850
Posted By JasperGeh
Basequality Dropoff

Hello people,

first time poster and also kind of first time sequencer.
I just started my PhD which involves a lot of NGS on a MiSeq and my supervisor and I ran 11 samples last week.

The...
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