User: Denis

gravatar for Denis
Denis30
Reputation:
30
Status:
New User
Location:
Russia, MSU
Last seen:
3 weeks ago
Joined:
4 years, 6 months ago
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s**********@gmail.com

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Posts by Denis

<prev • 46 results • page 1 of 5 • next >
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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 23 days 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 23 days 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 26 days 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 26 days ago by Denis30
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Extract SNPs flanking sequences based on VCF and genome Fasta files
... I have `VCF` file (containing diallelic variants) and reference genome in `Fasta` of some non-model plant. I'd like to extract `SNPs` flanking sequences. I've found that `bedtools` and `samtools faidx` could be to some extent useful, but apparently don't solve the issue. I need to get output (`fasta ...
genome sequence snp written 26 days ago by Denis30 • updated 23 days ago by Pierre Lindenbaum112k
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Extract SNPs from VCFfile located in genes based on GFF file information
... I have a `VCF` file with `SNPs` and genes subset of `GFF` file (only genes are present). How to extract `SNPs` in `VCF` format located in genes from my data? ...
gene snp written 29 days ago by Denis30 • updated 29 days ago by finswimmer5.3k
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A way to verify that GFF and Fasta files make a valid pair (came from the same project version)
... Sorry for the weird question. I have `GFF` and `Fasta` files. I'm looking for the way to check if they relate to the same project version, i.e. in the `GFF` file i have correct annotation for the sequences in `Fasta` file. Is it realistic task? ...
genome assembly written 4 weeks ago by Denis30
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5 follow
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Multiple testing correction in linear mixed models (MLM) for GWAS
... Hi all, I'm performing `GWAS` with `MLM` approach. I'm wondering which multiple testing correction method i have to apply to my `MLM` resulted p-values? ...
gwas written 6 weeks ago by Denis30 • updated 6 weeks ago by pfs250
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Comment: C: Different samples order in .ped and phynotype data files
... Hi Kevin! I'd like to clarify one more thing related to my post. I input into analysis phenotype data for all samples as a separate file. I followed by your advises and indicated `--indiv-sort` in my command line. But because of high missing genotype rate for a number of individuals, they were filte ...
written 6 weeks ago by Denis30
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Comment: C: Different samples order in .ped and phynotype data files
... Hi Kevin! Thank you so much! ...
written 6 weeks ago by Denis30

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