User: shinken123

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shinken12380
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México
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Posts by shinken123

<prev • 41 results • page 1 of 5 • next >
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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 11 days ago by shinken12380 • updated 11 days ago by chrchang5234.3k
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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 17 days ago by shinken12380
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Comment: C: calculate Per variant Heterozygosity from VCF file
... I made the SNP calling with GATK. ...
written 18 days 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 18 days ago by shinken12380
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Hapmap to vcf
... Hi all, I have a hapmap file from tassel and I want to convert it to a vcf. Tassel can convert the file but takes the major allele as the reference and the minor as the alternative. I want to use the reference genome for the reference alleles and set the alleles different from the reference genom ...
vcf hapmap convert written 12 weeks ago by shinken12380 • updated 12 weeks ago by RamRS19k
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Calculation of heterozygosity
... Hi everyone, I am calculating the proportion of heterozygous loci per individual using the next simple formula: number of heterozygous loci/number of genotyped loci I am using SNPs calls from illumina data and my values are close to 0.5. However these lines are supposed to be maize homozygou ...
genome next-gen sequencing written 4 months ago by shinken12380
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Perform of disco Snp with low coverage samples
... Hi All, I have some hundreds of pair end illumina fastq files with really low coverage 0.5x (Skim Seq). I am wondering if discoSNP could make a decent work calling SNPs from these samples. Or which software you recommend me? Would be good to be able to call SNPs using even a single read. Because ...
discosnp snp calling low coverage written 6 months ago by shinken12380 • updated 6 months ago by pierre.peterlongo830
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Comment: C: trying to reproduce mirbase blastn
... For some reason that doesn't work. ...
written 8 months ago by shinken12380
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trying to reproduce mirbase blastn
... Hi I am trying to reproduce blastn results from the mirbase webpage. Using this: blastn -query query -db db -max_target_seqs 100 -reward 5 -penalty -4 -num_threads 8 -word_size 4 -evalue 10 -outfmt "6 qseqid sseqid positive evalue" and blastn -query query -db db -task blastn-short -m ...
mirbase blastn written 8 months ago by shinken12380
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Ontology gramene releases
... Dear all, I am looking for a maize ontology gramene .ga file for maize. The only one that I can found is [here](ftp://ftp.gramene.org/pub/gramene/release-55/ontology/go/]) However is for release 55, and it looks that this release is for maize genome V4. If I want the .ga file for B73 RefGen_v3 w ...
gene assembly written 14 months ago by shinken12380

Latest awards to shinken123

Popular Question 5 weeks 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 12 weeks ago, created a question with more than 1,000 views. For GBS SNPs calling
Popular Question 4 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 13 months ago, created an answer with at least 3 up-votes. For A: Obtaining the top matches from blast

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