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Search: Posts Made By: finswimmer
Forum: Bioinformatics 08-26-2019, 09:17 PM
Replies: 1
Views: 508
Posted By finswimmer
Like this (https://www.biostars.org/p/367960/)?

Like this (https://www.biostars.org/p/367960/)?
Forum: Bioinformatics 08-11-2019, 12:36 PM
Replies: 8
Views: 1,126
Posted By finswimmer
bwa mem...

bwa mem (https://sourceforge.net/p/bio-bwa/mailman/message/30894287/)
Forum: Bioinformatics 05-22-2019, 10:13 AM
Replies: 1
Views: 623
Posted By finswimmer
Changing the file extenstion .bgz to .gz should...

Changing the file extenstion .bgz to .gz should solve the problem.
Forum: Bioinformatics 05-20-2019, 08:19 PM
Replies: 2
Views: 531
Posted By finswimmer
You probably have a bcf file rather than a vcf. ...

You probably have a bcf file rather than a vcf.

You can use bcftools to convert it if needed.

bcftools view input.bcf > output.vcf
Forum: Bioinformatics 01-01-2019, 12:04 PM
Replies: 1
Views: 717
Posted By finswimmer
This should be possible with some unix commands...

This should be possible with some unix commands and datamash (https://www.gnu.org/software/datamash/).

cat input.txt|paste - - - -|datamash transpose --output-delimiter , > output.txt

This...
Forum: Illumina/Solexa 11-16-2018, 06:06 AM
Replies: 1
Views: 909
Posted By finswimmer
The thumbnails are only in the Output Folder. And...

The thumbnails are only in the Output Folder. And this is the only difference between Output and Analyse folder.

So if you are interested in viewing the thumbnails within the MiSeq Analysis Viewer...
Forum: Bioinformatics 10-18-2018, 09:09 PM
Replies: 2
Views: 571
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, 08:13 PM
Replies: 1
Views: 666
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, 09:27 PM
Replies: 1
Views: 1,631
Posted By finswimmer
Question also posted on...

Question also posted on https://www.biostars.org/p/324077/.
Forum: Bioinformatics 06-27-2018, 01:40 AM
Replies: 1
Views: 673
Posted By finswimmer
Cross-posted on biostars...

Cross-posted on biostars (https://www.biostars.org/p/323306/).
Forum: Bioinformatics 06-25-2018, 10:57 PM
Replies: 3
Views: 1,585
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, 01:43 AM
Replies: 3
Views: 650
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, 09:23 PM
Replies: 3
Views: 650
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, 04:40 AM
Replies: 7
Views: 863
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, 08:00 PM
Replies: 1
Views: 969
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, 08:39 PM
Replies: 1
Views: 682
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, 07:59 PM
Replies: 7
Views: 1,541
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, 09:57 PM
Replies: 7
Views: 1,541
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, 08:16 PM
Replies: 6
Views: 7,148
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, 09:07 PM
Replies: 9
Views: 1,392
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, 08:11 PM
Replies: 9
Views: 1,392
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, 08:06 PM
Replies: 6
Views: 1,859
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, 01:30 AM
Replies: 9
Views: 2,002
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, 07:48 PM
Replies: 9
Views: 2,002
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, 01:43 AM
Replies: 14
Views: 19,354
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
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