User: nuketbilgen

gravatar for nuketbilgen
nuketbilgen30
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

<prev • 14 results • page 1 of 2 • next >
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how to GWAS of characters with normal distribution?
... 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 ...
gwas normal distribution association chracter written 14 months ago by nuketbilgen30 • updated 14 months ago by GabrielMontenegro420
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Answer: A: How to extract sequence from fasta by sequence similarity
... Hi, How about zipped fastq files? zgrep command is not working. :/ ...
written 23 months ago by nuketbilgen30
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SNP array liftover data with p values
... 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 ...
p value snp liftover written 2.8 years ago by nuketbilgen30 • updated 15 months ago by Biostar ♦♦ 20
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Comment: A: Fasta Alternate Reference Maker extracted fasta files are same as reference
... Hi,  Sorry for my late response. I have 3 genes in the vcf file.  Thank you. ...
written 3.1 years ago by nuketbilgen30
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Fasta Alternate Reference Maker extracted fasta files are same as reference
... 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 ...
gatk fastaalternatereferencemaker myposts written 3.1 years ago by nuketbilgen30 • updated 2.6 years ago by dsosa0
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Answer: A: variant annotation snpeff bosTau7 build
... 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 nuketbilgen30
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variant annotation snpeff bosTau7 build
... 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 ...
annotation snpeff variant bostaurus7 written 3.4 years ago by nuketbilgen30
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Comment: C: Same sample with seperete bam files
... OK. I will do as you say. That is kind of a puzzle though.  Thank you again. ...
written 3.4 years ago by nuketbilgen30
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Comment: C: Same sample with seperete bam files
... 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 nuketbilgen30
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Comment: C: Same sample with seperete bam files
... Hi again. It worked. Thank you. I did not get an error this time :)  Thank you very much!!!!! ...
written 3.4 years ago by nuketbilgen30

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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