User: fatma.mokhtar

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Posts by fatma.mokhtar

<prev • 30 results • page 1 of 3 • next >
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Removing samples from FAM file using PLINK
... Hello, I have created 3 files (bed, bim, and fam) using PLINK. In the Fam file, I have adjusted the gender: 1 for male and 2 for female. In the fam file, I have 3 duplicates samples, I would like to remove those samples, How can I do that? Thank you in advance, Fatma Mokhtar ...
snp written 11 days ago by fatma.mokhtar10
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Comment: C: PED file PLINK
... I have another question, the created FAM file looks like this; ![https://ibb.co/zn2Bg5x][1] Can I now change the gender to male:1 and femal:2? Because I know the gender of the participants? But in the file I know that position or column 5 there we have gender, where we have (0) now, not? I use ATOM ...
written 14 days ago by fatma.mokhtar10
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Comment: C: PED file PLINK
... I see my mistake now, it was with the file name. With the command, I have created 3 files: bed, bim, and fam files Thank you ...
written 14 days ago by fatma.mokhtar10
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Comment: C: PED file PLINK
... Thank you for your reply. I got an error: iMac-Fatma-Mokhtar:ArrayData fatma.mokhtar$ ./plink --Go_Cam --no-fid --no-parents --no-sex --no-pheno --make-bed --out myFileBinary PLINK v1.90b6.18 64-bit (16 Jun 2020) www.cog-genomics.org/plink/1.9/ (C) 2005-2020 Shaun Purcell, Chri ...
written 14 days ago by fatma.mokhtar10 • updated 14 days ago by genomax85k
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PED file PLINK
... Hello, I want to start with the quality control of my data, but some files are not complete I think; I have received this PED file (please see attached) https://ibb.co/029NR33 but I do not see all information that should be in: FID, IID, PID, MID,SEX,PHENO How can I change that? Do you thin ...
plink snp written 14 days ago by fatma.mokhtar10 • updated 14 days ago by zx87549.4k
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Genes on chromosome
... Hello, Is there a simple program where you can enter a set of genes (I have 10 genes). and then you get the location of the gene on the chromosome in one figure. So a figure with 22 chromosomes contains my gene of interest? Many thanks, Fatma Mokhtar ...
gene written 5 weeks ago by fatma.mokhtar10 • updated 5 weeks ago by lieven.sterck8.0k
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Export to PLINK file
... Hello, I have data in the Axiom analysis suite. I want to export the data in a PLINK form file. I want to use PLINK now, but before that, the sample attributes should contain: Index ID Family ID Individual ID Father ID Mother ID Sex Affection status I don't have all in ...
snp written 6 weeks ago by fatma.mokhtar10 • updated 6 weeks ago by chrchang5237.1k
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(Closed) Identify the Wild type of a SNP
... Hello all, I have a question about the wild type. In different articles, they mention the allele but not the wild type. For instance, I have the SNP (rs11887534) D19H. The alleles of this SNP are DD, DH, and HH​ How can I identify the wild type? **Please open this link I have uploaded the image, ...
snp written 7 weeks ago by fatma.mokhtar10
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Wild-Type and database SNPs effect
... Hi all, 1-How to identify the wild-type of an SNP? for instance the SNP D19H rs11887534 of ABCG8 gene, you have the DD, DH, and HH. I know here that DD is the wild type. But is there a database where all of this is clear for different genes? 2- Is there a database that clarifies the effect of SNPs ...
snp written 8 weeks ago by fatma.mokhtar10 • updated 7 weeks ago by ATpoint36k
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SNPs in the ABCG8 gene
... Hi: What is the difference between C54Y and Y54C in the ABCG8, or are those the same. In some studies they use (C54Y): -https://www.jlr.org/content/48/12/2607.long - https://portlandpress.com/clinsci/article-abstract/109/2/183/68210/ATP-binding-cassette-transporter-G8-M429V?redirectedFrom=fullte ...
snp written 3 months ago by fatma.mokhtar10

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