User: nuketbilgen
nuketbilgen • 30
- Reputation:
- 30
- Status:
- New User
- Location:
- United Kingdom
- Last seen:
- 10 months, 3 weeks ago
- Joined:
- 5 years, 9 months ago
- Email:
- n**********@gmail.com
Posts by nuketbilgen
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... 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 18 months ago by
nuketbilgen • 30
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... 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 18 months ago by
nuketbilgen • 30
• updated
18 months ago by
GenoMax ♦ 95k
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... 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 18 months ago by
nuketbilgen • 30
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... 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 ...
written 18 months ago by
nuketbilgen • 30
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... 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 ...
written 23 months ago by
nuketbilgen • 30
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... 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 2.0 years ago by
nuketbilgen • 30
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... 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 2.0 years ago by
nuketbilgen • 30
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... I installed it via conda now.
But I don't know how to run it cause I can not locate Platypus.py file. ...
written 2.0 years ago by
nuketbilgen • 30
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... 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 ...
written 2.0 years ago by
nuketbilgen • 30
• updated
2.0 years ago by
ATpoint ♦ 44k
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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 3.5 years ago by
nuketbilgen • 30
• updated
3.5 years ago by
GabrielMontenegro • 570
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