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Search: Posts Made By: finswimmer
Forum: Bioinformatics 10-18-2018, 10:09 PM
Replies: 2
Views: 313
Posted By finswimmer
Hello MNMoller, could you please describe...

Hello MNMoller,

could you please describe why you want to do this?

fin swimmer
Forum: Bioinformatics 08-08-2018, 09:13 PM
Replies: 1
Views: 404
Posted By finswimmer
Hello, why you crossposted this here on...

Hello,

why you crossposted this here on seqanswer, if you already get an answer/guess in biostars (https://www.biostars.org/p/331153).

If this answer isn't enough for you please give feedback...
Forum: General 06-30-2018, 10:27 PM
Replies: 1
Views: 1,263
Posted By finswimmer
Question also posted on...

Question also posted on https://www.biostars.org/p/324077/.
Forum: Bioinformatics 06-27-2018, 02:40 AM
Replies: 1
Views: 405
Posted By finswimmer
Cross-posted on biostars...

Cross-posted on biostars (https://www.biostars.org/p/323306/).
Forum: Bioinformatics 06-25-2018, 11:57 PM
Replies: 3
Views: 1,251
Posted By finswimmer
Hello, whether AT or TT is needed to be...

Hello,

whether AT or TT is needed to be pathogenic depends on the mode of inheritance. Is it dominant than it is enough if one allele has T, if it is recessive you need TT (or a second mutation in...
Forum: Bioinformatics 06-21-2018, 02:43 AM
Replies: 3
Views: 404
Posted By finswimmer
So you want to identify what base change is...

So you want to identify what base change is associated with the rs number?

Do you have a list of these identifiers, a vcf file, ...? How does your input look like?

Do you want a...
Forum: Bioinformatics 06-20-2018, 10:23 PM
Replies: 3
Views: 404
Posted By finswimmer
Hello juhuvn, what do you mean by "risk...

Hello juhuvn,

what do you mean by "risk allele".

fin swimmer
Forum: Bioinformatics 06-13-2018, 05:40 AM
Replies: 7
Views: 538
Posted By finswimmer
Hello, before you can start to answers your...

Hello,

before you can start to answers your question you have to get familiar with the fileformat. Let's analyse the format you show us.

In a fasta file each sequence information consist of a...
Forum: Sample Prep / Library Generation 05-30-2018, 09:00 PM
Replies: 1
Views: 517
Posted By finswimmer
Hello seqtechno1, I'm not aware of such a...

Hello seqtechno1,

I'm not aware of such a cycler. But having the lid temperature on 75C seems to me very low. For all kind of reaction we use 105C.

But I'm unsure whether this can lead to...
Forum: Bioinformatics 05-24-2018, 09:39 PM
Replies: 1
Views: 401
Posted By finswimmer
Hello bong28, are you banerjeeshayantan?...

Hello bong28,

are you banerjeeshayantan? There is a very similar question on biostars (https://www.biostars.org/p/311964/#315568).

fin swimmer
Forum: Bioinformatics 05-13-2018, 08:59 PM
Replies: 7
Views: 636
Posted By finswimmer
Yes, why they shouldn't? It's a documented...

Yes, why they shouldn't? It's a documented (http://www.htslib.org/doc/tabix.html) feature. The -p parameter is just a shorthand for this. So in the case above, it would also work to use "-p vcf" as...
Forum: Bioinformatics 05-12-2018, 10:57 PM
Replies: 7
Views: 636
Posted By finswimmer
Hello, these are just presets. One can...

Hello,



these are just presets. One can define in which column the chromosome (aka sequence name), begin and end position are located.

So if you have the chromosome name in the first...
Forum: Sample Prep / Library Generation 01-17-2018, 09:16 PM
Replies: 6
Views: 5,932
Posted By finswimmer
Hello, yes, because the PEG...

Hello,



yes, because the PEG concentration in the solution is the critical reagence in the size selection process. I've found a nice blog post about it some time ago here:...
Forum: Illumina/Solexa 12-07-2017, 10:07 PM
Replies: 9
Views: 979
Posted By finswimmer
Hello, to your question about how to avoid...

Hello,

to your question about how to avoid overclustering: What was the concentration of your Library at the end of of the LibPrep? Have you measure it with qubit? What is the average fragment...
Forum: Illumina/Solexa 12-06-2017, 09:11 PM
Replies: 9
Views: 979
Posted By finswimmer
Hello, Read 2 und 3 are the index read. As...

Hello,

Read 2 und 3 are the index read. As they have just a few cycles the Q30 is alway higher than in Read 1 und 4.

What was the Cluster density? Have you had better runs before? What kind of...
Forum: General 12-06-2017, 09:06 PM
Replies: 6
Views: 1,381
Posted By finswimmer
Hello, can you please explain a little bit...

Hello,

can you please explain a little bit more, why you think that this region is difficult to amplify? 11kb and a gc conten of 62% doesn't sound quite difficult to me.

fin swimmer
Forum: Illumina/Solexa 11-23-2017, 02:30 AM
Replies: 9
Views: 1,224
Posted By finswimmer
You're right. I didn't have a coffee at the time...

You're right. I didn't have a coffee at the time of writing ;)

fin swimmer
Forum: Illumina/Solexa 11-22-2017, 08:48 PM
Replies: 9
Views: 1,224
Posted By finswimmer
Beside the mentioned reason: If you have two...

Beside the mentioned reason: If you have two librarys with the same concentration but with different fragment size, this also means, that the total number of fragments in the library with the lower...
Forum: Illumina/Solexa 11-14-2017, 02:43 AM
Replies: 14
Views: 14,481
Posted By finswimmer
Ah, great! That's probably the reason why there...

Ah, great! That's probably the reason why there is a 72C step for three minutes right before the normal pcr cycle in the TruSight/NextTera Kits from Illumina.

Thanks a lot!

fin swimmer
Forum: Illumina/Solexa 11-13-2017, 09:33 PM
Replies: 14
Views: 14,481
Posted By finswimmer
Hello, in nearly every picture I see to...

Hello,

in nearly every picture I see to tagmentation, there is a gap between one adapter and the DNA. The other adapter seems to be directly added to the 3' end. How is this gap filled? It must be...
Forum: Illumina/Solexa 10-17-2017, 09:18 PM
Replies: 6
Views: 2,241
Posted By finswimmer
Hello, take a look at the cluster pictures....

Hello,

take a look at the cluster pictures. If you overcluster to much, the MiSeq cannot detect all clusters correctly and reports a much smaller number.

fin swimmer
Forum: Bioinformatics 10-14-2017, 01:54 PM
Replies: 126
Views: 48,123
Posted By finswimmer
Hello Brian, Do you recommend adapter...

Hello Brian,



Do you recommend adapter trimming prior use of bbmerge? I thought if I provide the adapter sequence to bbmerge, it can find those paires which completly overlap more easy.

fin...
Forum: Bioinformatics 09-07-2017, 10:22 PM
Replies: 4
Views: 913
Posted By finswimmer
Hello, can you post a screenshot of IGV in...

Hello,

can you post a screenshot of IGV in this region? If I found it correctly, this is a position in a homopolymer run (11xT) which is typical not easy to sequence, align and discover a variant....
Forum: Illumina/Solexa 09-07-2017, 11:03 AM
Replies: 3
Views: 887
Posted By finswimmer
Hello, are you sure you loaded 1.25nM?...

Hello,

are you sure you loaded 1.25nM? Normal final concentrations of the library on a MiSeq are between 8-16pM.

What was the concentration of the library at the end of the library preparation?...
Forum: Illumina/Solexa 09-03-2017, 10:32 PM
Replies: 3
Views: 887
Posted By finswimmer
Hello, how many samples have you pooled? In...

Hello,

how many samples have you pooled? In what concentration did you load your library? What was the resulting cluster density and cluster passing filter?

fin swimmer
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