User: mad.cichlids

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mad.cichlids120
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Posts by mad.cichlids

<prev • 44 results • page 1 of 5 • next >
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Answer: A: ASMap for the qtl/r data
... okay, finally figured it out. I checked the example file in the ASMap. the data is really just individual id with the genotype information. However, in the qtl data format, it usually consists of phenotype and genotype and indivudual id, when I pass the individual id information to the "id" argumen ...
written 1 day ago by mad.cichlids120
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Comment: C: ASMap for the qtl/r data
... Can you please elaborate this? When I check the mapthis$pheno, it is a matrix of all phenotype data. This is the part that is puzzling me, what would a "correct column" name to pass the id argument (which requires genotype information? Thanks! ...
written 1 day ago by mad.cichlids120
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ASMap for the qtl/r data
... Hi, I am trying to build a genetic map with "ASMap" package using the F2 intercross data. The dataformat was initially prepared for qtl package.And the data in the qtl/r package works just fine, but it produces an error in "ASMap". And I did use the convert2bcsft() function to convert it to the form ...
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Comment: C: what is in the fasta.fai
... Make a lot of sense now. Thank you so much. ...
written 6.6 years ago by mad.cichlids120
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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 6.6 years ago by mad.cichlids120
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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, th ...
written 6.6 years ago by mad.cichlids120 • updated 11 months ago by RamRS30k
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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 6.6 years ago by mad.cichlids120 • updated 6.5 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 6.7 years ago by mad.cichlids120
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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 6.7 years ago by mad.cichlids120
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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 6.7 years ago by mad.cichlids120

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