User: Abbas.M

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Abbas.M0
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Posts by Abbas.M

<prev • 12 results • page 1 of 2 • next >
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How to find the location of snps in a gene, whether it is in the promoter, intron, exon or 5'UTR region?
... Hello, I have a plant data of 300 varieties, on which I already performed GWAS. After GWAS, I have annotated the most significant snps to find candidate genes. I found some candidate genes that are predicted to be associated with my trait. Now, I want to find the haplotypes of those candidate gen ...
gene R snp genome written 7 days ago by Abbas.M0 • updated 7 days ago by Emily_Ensembl21k
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Comment: C: Is there any method to convert a text file to VCF format?
... Thanks for your response, and it is highly appreciated. Sorry to say, I want a vcf file for genome wide association. This way it will create only a text file. In my genotype data the snps are not coded as numerical. It is coded in alphabets such as GG, TT, NN etc. As in vcf, snps are coded as 0, ...
written 11 days ago by Abbas.M0
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Is there any method to convert a text file to VCF format?
... Hello, I want to convert a text file into vcf format, is there any script or any method to convert it into vcf? It is a snp data, which is not in any format. Following are the headers of my text file. Chromosome Position RefBase AltBase MAF RefBaseNum AltBaseNum Sample 1 Sample2 Sample3 High ...
gene R next-gen snp written 11 days ago by Abbas.M0 • updated 11 days ago by devarora320
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Comment: C: Setting a threshold based on effective number of independent Snps in GWAS.
... thank you so much for answering my question. I did LD pruning in plink, but i was not sure about it, whether we can set a threshold of gwas on the basis of LD pruned snps. Once again thanks ...
written 5 weeks ago by Abbas.M0
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Setting a threshold based on effective number of independent Snps in GWAS.
... I want to set a threshold of GWAS based on effect number of independent snps in my genotype data. As i read in literature, most of the recently published papers have set threshold by this way. At first they calculated effective number of independent snps in their snp data. Then applied a basic bon ...
gene R snp genome written 5 weeks ago by Abbas.M0 • updated 5 weeks ago by Nicolas Rosewick9.3k
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How to impute missing SNPs of genotypic data of plant species, without having HapMap reference panel?
... hello all, I have a SNP genotype data of 228 accessions of cotton, on which I want to do GWAS. The genotype data has a lot of missing SNPs, which should be imputed. I have calculated genotyping rate in plink, which is 0.72. My goal is to do GWAS. The genotype data is already published, and I down ...
genome R snp written 4 months ago by Abbas.M0 • updated 12 weeks ago by SiegmundWANG10
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Comment: A: Unrecognized flag in Plink2
... I got it, thank you for your quick response ...
written 5 months ago by Abbas.M0
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Unrecognized flag in Plink2
... Hello all, I have been trying to calculate linkage disequilibrium on plink2 in linux, but it is constantly showing an error, following is my command and error plink2 --file hapmap1 (this is the command that I typed) PLINK v2.00a3LM 64-bit Intel (31 Aug 2020) www.cog-genomics.org ...
genome snp written 5 months ago by Abbas.M0
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Comment: A: Which Genotype file format is it?
... Thank you so much for your quick response. However, i answered very late, and sorry for that. I read a lot of stuff and figure out that the genotype file that i have, doesnot follow any format. Actually, it is neither vcf nor any other format. I have converted it in hapmap, vcf and plink format. A ...
written 5 months ago by Abbas.M0
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Which Genotype file format is it?
... Chromosome Position RefBase AltBase MAF RefBaseNum AltBaseNum Sample 1 Sample2 Sample3 I am confused about this format. I have downloaded it from an online database. I looks like vcf format, but it is not supported by any software. ...
genome snp written 6 months ago by Abbas.M0

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