User: nataliagru1

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nataliagru130
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Posts by nataliagru1

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Comment: C: Vcftools Runs Of Homozygosity Option
... Hello! I too am running into the same issue! Can anyone explain this?!! Thank you! ...
written 3 months ago by nataliagru130
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Answer: A: PopGenome software: concatenating chromosomes and coalescent simulations
... Dear All, popgenome actually has an option to concatenate genome classes. Therefore you can put each chromosome into a class (genome_chr1.class, genome_chr2.class, genome_chr3.class, etc.) and merge all genome classes via concatenate.classes(genome_chr1.class, genome_chr2.class, genome_chr3.class). ...
written 3 months ago by nataliagru130 • updated 16 days ago by RamRS24k
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Is it acceptable to use ShapeIT for parasite genomes?
... Dear all, I am posting this question to BioStars community as I am trying to get a consensus on phasing softwares such as ShapeIT and IMPUTE2, Beagle etc. and their use and application on parasites genomic data (species that are diploid). For a recent experiment I wanted to use fineStructure to c ...
shapeit impute2 haplotype phasing beagle written 3 months ago by nataliagru130 • updated 7 weeks ago by Biostar ♦♦ 20
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Answer: A: formating for fineSTRUCTURE input
... Hello. You need to use a program such as ShapeIT or IMPUTE2 to phase your VCF file. ShapeIT takes VCF files as input and will output a phased file format which you will need to convert to chrompainter format (these scripts and tools are provided on fineStructure website). In addition everything I am ...
written 3 months ago by nataliagru130
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Answer: A: Generating genetic map file to use as input for shapeit
... It is actually rather challenging to produce a genetic map file from scratch. ShapeIT does have the option to exclude the genetic map and use a function --roh or "recombination rate". This is simply one value. You should be able to find a recombination rate value in scientific literature for the spe ...
written 4 months ago by nataliagru130
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Comment: C: PopGenome tutorial files
... Indeed I have attempted to contact them many times to no avail! ...
written 4 months ago by nataliagru130
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Comment: C: Generating genetic map file to use as input for shapeit
... It is actually rather challenging to produce a genetic map file from scratch. ShapeIT does have the option to exclude the genetic map and use a function --roh or "recombination rate". This is simply one value. You should be able to find a recombination rate value in scientific literature for the spe ...
written 4 months ago by nataliagru130
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Merge phased files from ShapeIT
... Dear all, I have used ShapeIT to phase several VCF files. Each vcf file corresponding to a chromosome since ShapeIT can only phase when the data is separated by chromosome. I now have outputted phased data for each chromosome as such trypanosome_chr1.phase, trypanosome_chr2.phase, etc. I am won ...
shapeit phasing written 4 months ago by nataliagru130 • updated 4 months ago by Charles Warden7.4k
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Comment: C: Generating genetic map file to use as input for shapeit
... I wish someone could answer this lol ...
written 4 months ago by nataliagru130
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Comment: C: Help Interpreting PopGenome sliding window analysis for nucleotide diversity?
... https://docserv.uni-duesseldorf.de/servlets/DerivateServlet/Derivate-35086/Dissertation_Bastian_Pfeifer.pdf Dr. Pfeifer's dissertation on the program for those who seek clarification. ...
written 4 months ago by nataliagru130

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