User: potassiumiodide0990

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Posts by potassiumiodide0990

<prev • 31 results • page 1 of 4 • next >
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Modeling of a protein with more than 1000 residues
... Hi! I have a protein sequence which is way more than 1000 aa residues. However, it does not have a crystal structure. So I obtained one from homology modeling. I used I-TASSER for this however I'm not very happy with models that have been generated. Secondly, I have to dock a small ligand to a spec ...
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Loading IMPUTE2 dosage data into plink/seq
... Hi! I'm trying to load the dosage data from IMPUTE2. It keeps giving me this error  pseq error : invalid dosage line entry, wrong number of rows I even tried to work with the mydata.dat example given on this site https://atgu.mgh.harvard.edu/plinkseq/dosage.shtml  But then it gives me the same ...
dosage plink/seq impute2 written 4.0 years ago by potassiumiodide099070 • updated 3.8 years ago by Vincent Laufer1.0k
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Comment: C: Ld Plot For Imputed Dosage Data
... Can you please elaborate on that? How did you exactly convert the allelic dosage to genotype data? ...
written 4.8 years ago by potassiumiodide099070
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Comment: C: Ld Plot For Imputed Dosage Data
... How did u plot the LD for the imputed data? I'm unable to in haploview ...
written 4.8 years ago by potassiumiodide099070
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Imputing phased beagle files using minimac
... Hello ! I have a multi-sample vcf that was phased using beagle. This serves as my reference. For my target, I generated a phased file from a multi-sample bed file. For running imputations, I want to use minimac. I tried but I'm stuck! BADLY. I generated .snps file from the .map file (for the refe ...
imputing minimac phasing beagle written 5.0 years ago by potassiumiodide099070
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Comment: C: Homozygous Indel/Snp & Heterozygous Indel/Snp
... Hi Ashutosh... I have a doubt though.. AAATTTGGGCTTTAAA - Reference genome (Chr 1) AAATTTGGGtTTTAAA - Non-reference genome (Chr 1 from father) AAATTTGGGaTTTAAA - Non-reference genome (Chr 1 from mother) In the above example t replaces C on father's Chr 1, a replaces C on mother's Chr1. Will thi ...
written 5.1 years ago by potassiumiodide099070
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Fq In Vcf
... Hi everyone! I'm a very very new to these variant formats. So please, kindly help me out. I have a SNP vcf file. And I need the hom and het variants. But I dont want to use the 012 output format of vcftools, its just too much of hassle. So I was thinking of using bcftools/samtools. I was thinking of ...
vcf samtools bcftools vcftools written 5.2 years ago by potassiumiodide099070 • updated 5.2 years ago by Ashutosh Pandey11k
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Comment: C: Vcf Format And Filtering
... ^^ you mean bcf format right? Coz I didnt find FQ tag in vcf format... ...
written 5.2 years ago by potassiumiodide099070
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Comment: C: Gene Set Analysis Software That Takes A Vcf As Input
... Hi Giovanni... just the list of SNPs will do... ...
written 5.2 years ago by potassiumiodide099070
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Gene Set Analysis Software That Takes A Vcf As Input
... I have generated a vcf file, and was wondering if there is any gene set analysis server/software that is available that takes the vcf file as an input. Even otherwise, what are the other gene analysis softwares available? Is cytoscape good enough? ...
vcftools written 5.2 years ago by potassiumiodide099070 • updated 5.2 years ago by Alex Reynolds28k

Latest awards to potassiumiodide0990

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Popular Question 2.9 years ago, created a question with more than 1,000 views. For Gene Set Analysis Software That Takes A Vcf As Input
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Popular Question 4.8 years ago, created a question with more than 1,000 views. For Installation Of Fftw 3.3.3 Using Cygwin

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