The check for the rating is already included. The marker is only one (because the pair/column is one)may be, that's the reason for not showing LD - just a guess
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
Hmmm... So the haplotype possibilities will be (0,0),(0,1),(1,0),(1,1). Right?
Upon further reflection, my previous answer of four was incorrect (which I've now changed to reduce confusion from other readers)... there are only two possible haplotypes (ways of describing the sequence on a single chromosome) at such a locus: 1 and 0. You need multiple markers to get non-trivial haplotypes.Last edited by gringer; 12-21-2011, 03:41 AM.
Comment
-
Hi gringer,
I tried to use Haploview as well, in Linkage Fromat, I loaded PED file to the Data File, and MAP file to Locus Information File, it gave the error message:
"File Error: Individual 6 in family L3 appears more than once".
I have 4 sisters all in the same family L3, the first 6 columns are same, I don't if this error happened due to that?
Thanks for the help.
Comment
-
If you have pedigree information, then that should be in the first four columns. Individual IDs within a family need to be unique. If you've got four sisters, then it should look something like this:
Code:L3 1 0 0 1 0 A A G G A C L3 2 0 0 2 0 A A A G 0 0 L3 3 1 2 2 0 A C G G A C L3 4 1 2 2 0 A A G G A A L3 5 1 2 2 0 A A G G A C L3 6 1 2 2 0 A A A G C C
Comment
-
Thanks gringer for your quick response. the family size is quite big, there are 16 members in the family, I personally separated the big family into three small ones, I am not sure if it is right? one small branch family has 3 generations, the second one has 2 generations, the third one has 1 generation (as I said, only 4 sisters).
For the pedigree ID, I gave L1, L2, L3, in each family, set up individual ID with unique one, for example
L1 10 0 0 1 1
L1 9 0 0 2 1
L1 2 10 9 1 2
L1 3 10 9 1 1
L1 4 10 9 1 1
L1 5 2 0 2 2
L1 6 2 0 2 2
L1 7 2 0 2 1
L1 8 2 0 2 1
L2 1 0 0 1 2
L2 15 1 0 1 1
L2 16 1 0 1 1
L3 11 0 0 2 1
L3 12 0 0 2 1
L3 13 0 0 2 1
L3 14 0 0 2 1
Or construct the pedigree as a big family, like
L1 10 0 0 1 1
L1 9 0 0 2 1
L1 2 10 9 1 2
L1 3 10 9 1 1
L1 4 10 9 1 1
L1 5 2 0 2 2
L1 6 2 0 2 2
L1 7 2 0 2 1
L1 8 2 0 2 1
L1 1 0 0 1 2
L1 15 1 0 1 1
L1 16 1 0 1 1
L1 11 0 0 2 1
L1 12 0 0 2 1
L1 13 0 0 2 1
L1 14 0 0 2 1
I used the second one to try it on Haploview, it has error message again with "Files contain zero valid individual."
Please see the attached pedigree structure.
Thanks a lot for the help.Attached FilesLast edited by emilyjia2000; 12-29-2011, 02:08 PM.
Comment
-
The error you mentioned was the following:
Originally posted by emilyjia2000 View Post"File Error: Individual 6 in family L3 appears more than once".
If you have access to a Linux command line, could you try the following command?
Code:grep '^L3[[:space:]]\+6' <PED file>
Comment
-
Originally posted by emilyjia2000 View Postin pedigree structure, the parents info must have both father and mother? for some subfamily, I only have either father or mother, not both of them. In that case, missing one of the parents could cause error?
Thanks a lot
Comment
-
Do you have any idea how to correct it?
I think a Mendelian inheritance error means that it's incredibly unlikely that the observed parental genotypes could cause the observed child genotypes. One example would be a child with 'A A', and both parents 'C C'. I suppose if you've got enough columns in your linkage file, the probability of such errors for every individual approaches 1.
These should really be warnings, rather than errors, because when you're playing around with thousands of genotypes, rare events are quite frequent. But then again, Merlin is not all that great when working with thousands of loci.
Comment
-
I probably figured out the problem, when I converted VCF to PED by vcftools, I didn't use one chromosome, which could mess up it. I am not so sure, but it could be one reason. The problem is that when I tried to use vcftools convert VCF to PED with only one chromosome, say chr4, nothing's generated, I don't know what's wrong?
Thanks for the help
Comment
-
Hello. I chanced across this forum and I wonder if I can ask a rather naive question. I recently used PLINK/ Haploview for understanding the data of the highly ranked SNPs in a GWAS analysis. I had planned to visualize my SNPs in LD blocks [and their proximity to genes of interest[, by using Haploview. Additionally, I used dbSNP to confirm the proximity of my SNPs to genes of potential interests.
Curiously enough, no matter how hard I have tried, I cannot get Haploview to show the same genes, that I can visualize when using dbSNP. I have tried repeatedly but with no satisfactory breakthrough. I would be so grateful if someone could have some suggestions on what I may be doing incorrectly.
I can also give a list of sequential steps [ as to what I am doing that is giving different results]
Thankyou for taking the time to read my question.
A.Z
Comment
-
Your questions are a bit unclear. Could you try being a bit more specific?
First, How do you want your data to look? How many genes / chromosomes do your data cover? I've attached a few examples from my thesis. For the ones with the D' squares, I've used the SVG export function of Haploview and manually added in the genes and tweaked the image using Inkscape. The chromosome plot is an alternative plot that shows the whole genome at a glance, based on figures in the first WTCCC GWAS paper.
Second, what have you tried doing? If using the information track download of Haploview, have you checked to make sure that the build number is correct?
Comment
Latest Articles
Collapse
-
by seqadmin
The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...-
Channel: Articles
04-22-2024, 07:01 AM -
-
by seqadmin
Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...-
Channel: Articles
04-04-2024, 04:25 PM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, 04-11-2024, 12:08 PM
|
0 responses
59 views
0 likes
|
Last Post
by seqadmin
04-11-2024, 12:08 PM
|
||
Started by seqadmin, 04-10-2024, 10:19 PM
|
0 responses
57 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 10:19 PM
|
||
Started by seqadmin, 04-10-2024, 09:21 AM
|
0 responses
51 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 09:21 AM
|
||
Started by seqadmin, 04-04-2024, 09:00 AM
|
0 responses
56 views
0 likes
|
Last Post
by seqadmin
04-04-2024, 09:00 AM
|
Comment