User: mad.cichlids

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mad.cichlids100
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Posts by mad.cichlids

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Comment: C: what is in the fasta.fai
... Make a lot of sense now. Thank you so much. ...
written 5.2 years ago by mad.cichlids100
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Comment: C: what is in the fasta.fai
... This helped a lot! in other words, the SNP position in the genome is really depend on how the contigs are organized or aligned up with other contigs in the genome? ...
written 5.2 years ago by mad.cichlids100
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Comment: C: what is in the fasta.fai
... Just out of curious, about information in the column3, say "gi|394055774|gb|AGTA02000001.1|    5516    93    70    71" has a length of 5516, starts from 93, would not I expect the next contig approximately starts from the position 5516 + 93 = 5609, in reality it starts from 5781, likewise, the nex ...
written 5.2 years ago by mad.cichlids100
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what is in the fasta.fai
... Hi, this may sounds a bit trivial question, i indexed my ref genome, along with the indexed genome, there is also a file called .fasta.fai. My question is what is in the fasta.fai? I opened this file, it does not have any header. Did I do anything wrong ? I then used the ref genome to call SNPs. I ...
bowtie written 5.2 years ago by mad.cichlids100 • updated 5.1 years ago by Biostar ♦♦ 20
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Answer: A: Extract Dp From The Vcf File
... Thanks to Valerie Obenchain's help, it turned out that it is the colon sign in the INFO column caused this, after replacing the colon with semicolon, everything works fine. ...
written 5.3 years ago by mad.cichlids100
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Comment: C: Extract Dp From The Vcf File
... Thanks. I used vcf <- readVcf("z.vcf", "Genome"), z.vcf is my vcf file, "Genome" is the folder of my indexed ref genome. The package is variantannotation in Bioconductor. Here is how i installed it: source("http://bioconductor.org/biocLite.R") biocLite("VariantAnnotation") According to t ...
written 5.3 years ago by mad.cichlids100
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Extract Dp From The Vcf File
... I want to extract some information from the info column of my VCF file, when I load my VCF file, I do not have access to my depth (DP) and number of alleles (AN), however, the NS(number of samples for this allele works fine), DP and AN shown as "NA". My vcf file clearly show that neither DP nor AN i ...
vcf R written 5.3 years ago by mad.cichlids100
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Parentage Analysis Vs Pedigree Analysis
... Hi, I recently generated a vcf file, which includes one pair of grandparents (two different species), several parents(hybrids derived from grandparents of two different species), and large number of f2 (interbreeding of F1s). But the parents of F2s are unknown, need to be inferred from the genotyp ...
vcf R written 5.3 years ago by mad.cichlids100 • updated 5.1 years ago by Biostar ♦♦ 20
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Comment: C: Vcftools Blank Output
... Thank you, Giovanni, I did check the out file. It is an empty doc with a header "CHROM BIN_START N_SNPS TajimaD" ...
written 5.3 years ago by mad.cichlids100
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Vcftools Blank Output
... Hi, I am trying to use the vcftools to get some summary statistics about my VCF file. When I was using the following functions: zcat my.sorted.vcf.gz | vcftools --vcf - --het --out het zcat my.sorted.vcf.gz | vcftools --vcf - --TajimaD 20 --out TajimaD The tool did not give out any results but a ...
vcf written 5.3 years ago by mad.cichlids100

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