User: nuketbilgen

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nuketbilgen30
Reputation:
30
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New User
Location:
United Kingdom
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2 weeks, 4 days ago
Joined:
4 years, 9 months ago
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Posts by nuketbilgen

<prev • 23 results • page 1 of 3 • next >
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Comment: C: Contig name difference due to reference genome
... Hi again, vcf files generated by GATK haplotypecaller walker. Haplotype Calling java -jar GenomeAnalysisTK-3.3-0/GenomeAnalysisTK.jar -T HaplotypeCaller -R all.chrs.con.fa -L TEST_Chr01 -I aligned_reads.sorted.dedup.bam --emitRefConfidence GVCF --variant_index_type LINEAR -- variant_index_parameter ...
written 6 months ago by nuketbilgen30
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Comment: A: Contig name difference due to reference genome
... I know its a long shot, but would you suggest that I merge the files according to their chrs? like this? I=PasaHardFiltered.chrA1_NW_019365239v1_random.vcf I=PasaHardFiltered.chrA1_NW_019365240v1_random.vcf I=PasaHardFiltered.chrA1_NW_019365241v1_random.vcf I=PasaHardFiltered.chrA1_NW_019365243 ...
written 6 months ago by nuketbilgen30 • updated 6 months ago by genomax77k
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Comment: C: Contig name difference due to reference genome
... exactly yes. When I split vcf files into chr by SnpSift split command, I got 40 files for felcat9.fa aligned files, and I got 426 files for NCBI one. I worry to lose important variants... ...
written 6 months ago by nuketbilgen30
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Contig name difference due to reference genome
... Hi everyone, I have vcf files of 4 feline genomes, but in vcf header I see different contig names. I checked the reference genome file line, you can see it below. reference=file:///ifswh1/BC_COM_P1/F18FTSEUHT0898/CATsxlR/analysis/index/GCF_000181335.3_Felis_catus_9.0_genomic.fa reference=f ...
genome next-gen alignment written 6 months ago by nuketbilgen30
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Would haplotype analysis is enough for a rare disease?
... Hi, I want to analyze the WGS data from the following work, - the aim of the project finding a pathogenic variant. - samples are core family (father, mother and two affected offspring) and one nonfamily member. - penetrance is observed in the sample group, (female offspring affected severely and m ...
genome next-gen haplotype rare disease written 10 months ago by nuketbilgen30
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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 12 months 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 12 months 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 12 months 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 12 months ago by nuketbilgen30 • updated 12 months ago by ATpoint28k
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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 2.5 years ago by nuketbilgen30 • updated 2.5 years ago by GabrielMontenegro540

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Popular Question 4 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 2.5 years ago, created a question with more than 1,000 views. For Fasta Alternate Reference Maker extracted fasta files are same as reference
Popular Question 2.5 years ago, created a question with more than 1,000 views. For variant annotation snpeff bosTau7 build
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Fasta Alternate Reference Maker extracted fasta files are same as reference
Popular Question 4.1 years ago, created a question with more than 1,000 views. For Same sample with seperete bam files

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