User: Denis

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Denis30
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Posts by Denis

<prev • 52 results • page 1 of 6 • next >
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Interpretation of Tassel MLM output
... I've performermed `GWAS` by `MLM` in `Tassel` and got a tables with results. What is the meaning and biological interpretation of `Effect` and `MarkerR2` columns of tables below (short example): Table1 Trait Marker Locus Site Allele Effect Obs H S01_13979 1 13979 C -2,34E+01 57 H S01_13 ...
genome gwas snp written 7 hours ago by Denis30
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Comment: C: PLINK Haplotype blocks estimation not working
... I've solved the issue by adding `--blocks no-pheno-req` to the plink 1.9 command line. ...
written 19 days ago by Denis30
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Calculate a square matrix of r2 between all SNPs in genome during LD analysis
... I have a multiple genotypes in `vcf` format. I'd like to calculate a square matrix of `r2` between each pair of SNPs in genome (even for these located in differen chromosomes). Below is a toy example i wish to get: rs1 rs2 rs3 rs1 1 0.8 0.3 rs2 0.8 1 0. ...
genome R snp written 19 days ago by Denis30
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Comment: C: LD-decay in a r2 vs distance(cm) plot
... Thanks for sharing that! It helped me a lot! Let me a question please? 1) You created mid column in the command: dfr1 <- dfr1 %>% mutate(start=as.integer(str_extract(str_replace_all(distc,"[\\(\\)\\[\\]]",""),"^[0-9-e+.]+")), end=as.integer(str_extract(str_repl ...
written 19 days ago by Denis30
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Comment: C: Compute Phylogenetic Trees Using Snps Data (VCF files)
... Hi, i'm curious,if the `SNPRelate` will give bootstrap values along with a tree? If i'm correct i tried a `SNPhylo` several years ago, but was not able to get any tree. Recently i've converted `VCF` file to `Hapmap` and then by means of `R`/`Bash` scripting converted it to the `fasta` alignment even ...
written 25 days ago by Denis30
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Comment: C: Compute Phylogenetic Trees Using Snps Data (VCF files)
... I'm looking for the similar software, but i need a tree with bootstrap supports. Do you know any ready solution? Tassel doesn't do that unfortunately. ...
written 25 days ago by Denis30
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Answer: A: Extract SNPs flanking sequences based on VCF and genome Fasta files
... Improved version from __future__ import print_function import pysam vcf = pysam.VariantFile("Sun_CDS.vcf") genome = pysam.FastaFile("genome.fasta") flank=62 with open("SNP_CDS.txt", "w") as f: ...
written 11 weeks ago by Denis30
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Comment: C: Extract SNPs flanking sequences based on VCF and genome Fasta files
... Hello finswimmer! Agree! Many thanks for your comments! They are extremely useful. I've changed the code (added `with` statement). Please see the newer version below. I'm wondering how can i adjust the code regarding your the 4-th point? Could you do it please? ...
written 11 weeks ago by Denis30
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Answer: A: Extract SNPs flanking sequences based on VCF and genome Fasta files
... I slightly modified the script provided by finswimmer. Now it's compatible with python 2.X, writes output to the text file instead of STDOUT. Besides, ID of each SNP is present in output file as separate field. Probably, some additional optimisation and syntax polishing are required, but even this v ...
written 11 weeks ago by Denis30
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Comment: C: Extract SNPs flanking sequences based on VCF and genome Fasta files
... @finswimmer Hi! Many thanks. I need some time for the code understanding. ...
written 11 weeks ago by Denis30

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