User: nuketbilgen

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nuketbilgen30
Reputation:
30
Status:
New User
Location:
United Kingdom
Last seen:
3 days, 18 hours ago
Joined:
3 years, 9 months ago
Email:
n**********@gmail.com

Posts by nuketbilgen

<prev • 18 results • page 1 of 2 • next >
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Comment: C: Platypus variantcaller.c:16971 errpr
... As you have said, it is working. but now I get this error. print "\n\n%s command is not yet implemented\n\n" %(x) ^ SyntaxError: invalid syntax ...
written 24 days ago by nuketbilgen30
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Comment: C: Platypus variantcaller.c:16971 errpr
... I can find it in /home/nuketbilgen/anaconda3/envs/**my_env**/bin/platypus as a link to program. Is it a problem that I have installed it into my_env? ...
written 26 days ago by nuketbilgen30
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Comment: C: Platypus variantcaller.c:16971 errpr
... I installed it via conda now. But I don't know how to run it cause I can not locate Platypus.py file. ...
written 26 days ago by nuketbilgen30
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Platypus variantcaller.c:16971 errpr
... Hi everyone. I am trying to use Platypus for variant calling. even though I have tried everything I could to fix it (moved htslib to usr/local, exported paths to it) I always got the following error. I deleted and reinstalled platypus and htslib as well. could you help me, please? python Pla ...
variantcaller.c:16971 platypus written 26 days ago by nuketbilgen30 • updated 26 days ago by ATpoint13k
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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 19 months ago by nuketbilgen30 • updated 19 months ago by GabrielMontenegro500
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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 2.3 years 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 3.2 years ago by nuketbilgen30 • updated 19 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 3.5 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 3.5 years ago by nuketbilgen30 • updated 2.9 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 3.7 years ago by nuketbilgen30

Latest awards to nuketbilgen

Popular Question 19 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 19 months ago, created a question with more than 1,000 views. For variant annotation snpeff bosTau7 build
Popular Question 19 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 3.1 years ago, created a question with more than 1,000 views. For Same sample with seperete bam files

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