User: dirranrak

gravatar for dirranrak
dirranrak10
Reputation:
10
Status:
New User
Location:
United States
Last seen:
2 months, 2 weeks ago
Joined:
2 years, 7 months ago
Email:
d********@gmail.com

Posts by dirranrak

<prev • 34 results • page 1 of 4 • next >
0
votes
0
answers
296
views
0
answers
Comment: A: Recoding plink file from 12 to 01
... Hi, sorry for not giving enough details. I am trying to use finestructure, I need chromopainter file to be able to work with. I have plink ped file recoded 12, I need to convert the plink file into chromopainter format by using plink2chromopainter.pl. I followed the instruction from the finestructur ...
written 3 months ago by dirranrak10
0
votes
0
answers
296
views
0
answers
Recoding plink file from 12 to 01
... Hi all, I tried to use Plink2chromopainter.pl to convert plink file to chromopainter file. I have plink file recoded 12 but I need to recode the file to 01 before using the program. I did use --recode 01 --output-missing-genoty 3. I have red the plink manual but I still got a strange content in the ...
file plink2chromopaiter.pl conversion plink written 3 months ago by dirranrak10 • updated 3 months ago by Ram14k
0
votes
0
answers
533
views
0
answers
Comment: C: CV error in admixture and submiting the job on the cluster
... Thank you Jean-Karim Heriche, the cluster itself solved the problem, I did not do something wrong apparently. Might be something wrong within the system. Thank you very much ...
written 22 months ago by dirranrak10
0
votes
0
answers
533
views
0
answers
CV error in admixture and submiting the job on the cluster
... Hi all, I am trying to estimate the lowest CV by using what is in page 4 of the manual. It is working well when I use the script on my local computer. But when I try to submit a job on the cluster, the cluster accepts only the very basic script which "./admixture file K" however, it does not accep ...
human population genetics cv error admixture hpc written 22 months ago by dirranrak10
0
votes
0
answers
818
views
0
answers
Plink to Treemix
... Hi all, I tried to convert Plink file to Treemix file, I remarked that in the note at different websites you need to get a .frq file from using --freq --within flag in Plink. But the thing is that when you use the these flags in the same run, you get a .frq.strat file but not only .frq. I followed ...
plink treemix written 22 months ago by dirranrak10
0
votes
1
answer
570
views
1
answers
Comment: C: Filtering data after bmerge in plink
... Hi chrchang523, Thank you for your answer. Does it mean that it is no need to test the quality of the merged dataset? and what should be the best way to minimize bias? ...
written 23 months ago by dirranrak10
1
vote
1
answer
570
views
1
answer
Filtering data after bmerge in plink
... Hi all, After filtering and merging data from using --bmerge flag in Plink 1.9, I did use the same thresholds as before merging the dataset to test the quality of the merged dataset. Then I have this "error: All people removed due to missing genotype data (--mind)". Why I loose the quality that I h ...
threshold plink snp written 23 months ago by dirranrak10 • updated 23 months ago by chrchang5233.1k
0
votes
0
answers
498
views
0
answers
Trouble running ALDER
... Hello all, I have convert plink file ped and map to eigenstrat file using convertf to be used on ALDER. When I run the converted files, I got fatalx: no real map. I don't know if it is related to make fail error when compiling the program. I installed FFTW3 and LAPACK as required but I don't unders ...
alder plink convertf written 23 months ago by dirranrak10 • updated 21 months ago by Biostar ♦♦ 20
0
votes
2
answers
5.0k
views
2
answers
Comment: C: ADMIXTURE and R, color meaning on barplot in studing population ancestry, K valu
... Hi Zev, Thank you for the code. I was busy to understand learning coding other stuff. But now when I try to run your code in R, even just at the beginning I got the error below. And if I remove the quote when specifying the directory, the rest of the code becomes comment. plot.admixture<-funct ...
written 23 months ago by dirranrak10
0
votes
0
answers
599
views
0
answers
What should be the base line for merging data from different platforms in plink?
... Hi all, I have some genotype datasets from Illumina and Affymetrix, I am a bit confused because I still have an abnormal pca plot after merging the data using --bmerge with plink. They are in ATGC allele. What I did: get the Pan Asian dataset (Affymetrix 50k_Xba Gene chip), recode the 0,1,2,9 alle ...
platforms plink written 2.0 years ago by dirranrak10

Latest awards to dirranrak

Great Question 21 months ago, created a question with more than 5,000 views. For Find mismatch in two columns in a data frame in R
Epic Question 21 months ago, created a question with more than 10,000 views. For Find mismatch in two columns in a data frame in R
Popular Question 21 months ago, created a question with more than 1,000 views. For Find mismatch in two columns in a data frame in R
Popular Question 21 months ago, created a question with more than 1,000 views. For Calculate the Fst between populations
Popular Question 21 months ago, created a question with more than 1,000 views. For Warning: different physical position for rs365066
Popular Question 2.1 years ago, created a question with more than 1,000 views. For ADMIXTURE and R, color meaning on barplot in studing population ancestry, K value

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1088 users visited in the last hour