User: shinken123

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shinken12380
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México
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1 month, 3 weeks ago
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3 years, 11 months ago
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Posts by shinken123

<prev • 47 results • page 1 of 5 • next >
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Comment: C: What is an illumina technical sequence?
... Thanks. I am asking this because is very clear what is an adapter, but I can not find the definition anywhere for a technical sequence. Cheers ...
written 7 weeks ago by shinken12380
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(Closed) What is an illumina technical sequence?
... Hi all, I am using trimmomatic and in their manual [here](http://www.usadellab.org/cms/?page=trimmomatic) they mention adapters and technical sequences.Could some one please tell me what is a technical sequence? I can not find info about this. Thank you in advance. ...
sequencing written 7 weeks ago by shinken12380
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Haploview Skipping block output: no valid blocks error
... Hi all, I am runnig haploview https://www.broadinstitute.org/haploview/haploview and I am having the next output: ***************************************************** Haploview 4.2 Java Version: 1.8.0_201 ***************************************************** Arguments: -nogui -pedfile ...
software error snp written 9 weeks ago by shinken12380
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Answer: A: Haploview error (Hapmap data format error)
... At the end I upload my file in to TASSEL in hapmap format, I convert it to plink format using TASSEL, then I change the -9 for 0 using seed, then Haploview was able to read this data. I hope that this could help some one. ...
written 9 weeks ago by shinken12380
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Comment: C: Haploview error (Hapmap data format error)
... I have exactly the same problem, did you figure out how to solve it? ...
written 12 weeks ago by shinken12380
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Haplotype visualization from postion data
... Hi all, I have haplotypes from which I could extract their position (chromosome, start, end) and add a colour. Using this info there is a software that coudl help me to visualize the haplotypes? Best Wishes, Eric ...
genome sequence snp written 3 months ago by shinken12380 • updated 7 weeks ago by Biostar ♦♦ 20
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Convert matrix in numeric format to genotype format
... Hi All, I want to convert a matrix in numeric format, 0 for homozygous reference allele, 1 for heterozygous and 2 for homozygous alternative to a genotype matrix, if it is possible to a vcf file. Do you know any tool to do it? Best Wishes, Eric ...
snp written 7 months ago by shinken12380 • updated 7 months ago by chrchang5235.4k
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Comment: C: calculate Per variant Heterozygosity from VCF file
... Yep, thats True, I this case, because my file is not phased, the solution was to use your script only with the nonphases counts. like this gsub(/0\/1|1\/0/,""). Thank you for your script It help me a lot. ...
written 7 months ago by shinken12380
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Comment: C: calculate Per variant Heterozygosity from VCF file
... I made the SNP calling with GATK. ...
written 7 months ago by shinken12380
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Comment: C: calculate Per variant Heterozygosity from VCF file
... This is almost perfect. The problem are sites like this: 0/1:1,1:2:26:0|1:27975_T_C:39,0,26 This site gives me two heterozygous counts instead of 1, I am trying to solve it, adding to gsub something like this but is not working gsub(/^0\|1|^1\|0|^0\/1|^1\/0/,"") Any Idea? ...
written 7 months ago by shinken12380

Latest awards to shinken123

Popular Question 8 weeks ago, created a question with more than 1,000 views. For mapping quality for sanger reads
Popular Question 7 months ago, created a question with more than 1,000 views. For mapping quality for sanger reads
Popular Question 7 months ago, created a question with more than 1,000 views. For Remove a list of positions form a VCF file
Popular Question 8 months ago, created a question with more than 1,000 views. For vcf-merge is giving me a few SNPs in the merged vcf file
Popular Question 9 months ago, created a question with more than 1,000 views. For GBS SNPs calling
Popular Question 11 months ago, created a question with more than 1,000 views. For vcf-merge is giving me a few SNPs in the merged vcf file
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Obtaining the top matches from blast

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