User: nuketbilgen
nuketbilgen • 30
- Reputation:
- 30
- Status:
- New User
- Location:
- United Kingdom
- Last seen:
- 1 week ago
- Joined:
- 3 years, 5 months ago
- Email:
- n**********@gmail.com
Posts by nuketbilgen
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... Hi everyone,
I have a canine SNP array results from affymetrix, need to make an GWAS between SNP results and characters which has normal distribution. Since I can not divide my results in to two groups I don't know what to do and how to approach to the data sets. I would be glad if you could sugges ...
written 14 months ago by
nuketbilgen • 30
• updated
14 months ago by
GabrielMontenegro • 420
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... Hi,
How about zipped fastq files?
zgrep command is not working. :/ ...
written 23 months ago by
nuketbilgen • 30
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... Hi,
We have canine snp array data (CanineSNPHD, ILLUMINA). The positions of the snps in this array are for Canine 2 genome version. So we need to convert this data to canine 3 gv. We used UCSC but it does not take the p values thus we need to delete row by row. It has been exhausting.
I hope tha ...
written 2.8 years ago by
nuketbilgen • 30
• updated
15 months ago by
Biostar ♦♦ 20
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... Hi,
Sorry for my late response.
I have 3 genes in the vcf file.
Thank you.
...
written 3.1 years ago by
nuketbilgen • 30
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... Hi!
I need to extract fasta sequences for two genes. I used
java -jar /Users/nuketbilgen/programs/GenomeAnalysisTK-3.3-0/GenomeAnalysisTK.jar -T FastaAlternateReferenceMaker -R $REF -o YK20.fasta -L bTau7_2and6_subset.bed -V YK20_S24S12.raw.g.vcf
but it does not seem to work all of the output fa ...
written 3.1 years ago by
nuketbilgen • 30
• updated
2.6 years ago by
dsosa • 0
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... Hi everyone,
I solved it! just needed to ad -c snpEffect.config
java -jar snpEff.jar build -c snpEffect.config -refSeq -v bosTau7
...
written 3.4 years ago by
nuketbilgen • 30
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... Hi everyone!
The highly unlikely situation happened.
My next generation seq. data have been aligned to bosTau7 build.
I am having troubles on building data set for that. And when I use lift up the vcf file with USCS bosTau7 build to UMD3.1 snpeff does not give me any annotation (the error diffe ...
written 3.4 years ago by
nuketbilgen • 30
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... OK. I will do as you say. That is kind of a puzzle though.
Thank you again.
...
written 3.4 years ago by
nuketbilgen • 30
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... Will do that. And one more question, If I have 4 samples to merge than I would just add SM:N s like this?
s/SM:N17/SM:N15/SM:N14/SM:N16/
...
written 3.4 years ago by
nuketbilgen • 30
0
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... Hi again.
It worked. Thank you. I did not get an error this time :)
Thank you very much!!!!!
...
written 3.4 years ago by
nuketbilgen • 30
Latest awards to nuketbilgen
Popular Question
14 months ago,
created a question with more than 1,000 views.
For Fasta Alternate Reference Maker extracted fasta files are same as reference
Popular Question
14 months ago,
created a question with more than 1,000 views.
For variant annotation snpeff bosTau7 build
Popular Question
15 months ago,
created a question with more than 1,000 views.
For Fasta Alternate Reference Maker extracted fasta files are same as reference
Popular Question
2.8 years ago,
created a question with more than 1,000 views.
For Same sample with seperete bam files
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