User: boymin2020

gravatar for boymin2020
boymin202020
Reputation:
20
Status:
New User
Location:
Last seen:
2 months, 3 weeks ago
Joined:
3 years, 2 months ago
Email:
b*********@gmail.com

Posts by boymin2020

<prev • 33 results • page 1 of 4 • next >
0
votes
1
answer
169
views
1
answers
Comment: C: convention from vcf to plink
... Got it, thanks for the tips. ...
written 3 months ago by boymin202020
0
votes
1
answer
169
views
1
answers
Comment: C: convention from vcf to plink
... I tried, nothing changed. ...
written 3 months ago by boymin202020
2
votes
1
answer
169
views
1
answer
convention from vcf to plink
... Hi, I want to just keep SNPs during the vcf2plink conversion, this is the command: plink1.9 --noweb --vcf ${vcf_fil} --double-id --biallelic-only --snps-only just-acgt --make-bed --out The error is Error: Invalid --snps-only parameter ‘just-acgt’. Does anyone encounter the same issue. ...
plink written 3 months ago by boymin202020 • updated 3 months ago by chrchang5235.5k
0
votes
0
answers
171
views
0
answers
Input for -w options of smartpca.perl
... Hi, I am doing SNP-array data QC with Anderson's paper on nature protocol.https://www.nature.com/articles/nprot.2010.116 However, its supplement data cannot be downloaded now which make me confused about a file named "pca-populations.txt". It will be very appreciated if anyone can give a copy of th ...
smartpca written 6 months ago by boymin202020
1
vote
1
answer
303
views
1
answer
Questions about gene length and GC content in CQN normaliztion
... Hi, There are several questions after I read the manual of CQN normalization method. Although I also have checked several related posts of Biostar, but still confused a lot. 1. How to get the information of gene length? I think it is easy to calculate as the gene bands can be obtained directly fro ...
gc content cqn rna-seq gene length written 9 months ago by boymin202020 • updated 7 months ago by rrbutleriii70
0
votes
1
answer
1.2k
views
1
answers
Comment: C: Question about the reliability of --check-sex in PLINK2
... Thank you very much. ...
written 12 months ago by boymin202020
0
votes
1
answer
1.2k
views
1
answers
Comment: C: Question about the reliability of --check-sex in PLINK2
... 1. Use --freq to get the MAF report, then extract variants (>0.01) with rs outside of PAR? ...
written 12 months ago by boymin202020
0
votes
1
answer
1.2k
views
1
answers
Comment: C: Question about the reliability of --check-sex in PLINK2
... Thanks for your reply. Another two questions. 1. How the select the specific set of SNPs? 2. What is the meaning of PAR? ...
written 12 months ago by boymin202020 • updated 12 months ago by RamRS24k
2
votes
1
answer
1.2k
views
1
answer
Question about the reliability of --check-sex in PLINK2
... Hi all, I have tried to use plink2 to check the gender situation of my several datasets. It always shows more problem samples than expected. For some datasets, I also have RNAseq data. Then I checked again with some genes just on chromosome X or Y. It turned out a few problem samples. Therefore, I ...
plink2 sex-check written 12 months ago by boymin202020 • updated 12 months ago by chrchang5235.5k
0
votes
1
answer
395
views
1
answers
Comment: C: Chromosome lost after merge with vcf-merge
... Yes. Thanks for the follow-up. ...
written 13 months ago by boymin202020

Latest awards to boymin2020

Popular Question 4 months ago, created a question with more than 1,000 views. For Difference between SNParray genotype dataset and WES genotype dataset
Popular Question 4 months ago, created a question with more than 1,000 views. For Memory usage of picard Samsort
Supporter 9 months ago, voted at least 25 times.
Popular Question 10 months ago, created a question with more than 1,000 views. For Java memory issue in GATK
Popular Question 11 months ago, created a question with more than 1,000 views. For Memory usage of picard Samsort

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1153 users visited in the last hour