User: mbyvcm

gravatar for mbyvcm
mbyvcm260
Reputation:
260
Status:
Trusted
Location:
USA
Last seen:
8 hours ago
Joined:
1 year, 6 months ago
Email:
c****************@gmail.com

Posts by mbyvcm

<prev • 39 results • page 1 of 4 • next >
0
votes
1
answer
121
views
1
answers
Answer: A: PLINK- chromosome ID disappears after running association tests
... The first column is CHR and the second is SNPID. Have you got these the wrong way around? I think that chromosome has to be numeric and, because yours is not ["supercont1.1004_pilon"], it is returning a null ('0') chromosome value. You are probably also correct that only a chromosome value between ...
written 3 days ago by mbyvcm260
3
votes
1
answer
169
views
1
answers
Answer: A: Is there a quick method to extract regularly-spaced features/SNPs from a VCF fil
... I'm not sure I fully understand why you want to arbitrarily select SNPs at a given distance. But I think you may be looking for the "--thin" flag in [VCFtools][1]. Also take a look at [this][2]. I have never used it, but I hope it helps. [1]: http://vcftools.sourceforge.net/ [2]: https://sourc ...
written 4 days ago by mbyvcm260
0
votes
1
answer
120
views
1
answers
Comment: C: finding the gene contain the snps ID
... If you follow the link and look at the PDF documents ('GenomicRanges HOWTOs') halfway down the page, all will be revealed! This does require some knowledge of R, but a little time spent now is, in my honest opinion, well worth it. ...
written 4 days ago by mbyvcm260
1
vote
1
answer
120
views
1
answers
Answer: A: finding the gene contain the snps ID
... For these types of genome annotation tasks [GRanges][1] is great. [1]: https://bioconductor.org/packages/release/bioc/html/GenomicRanges.html ...
written 5 days ago by mbyvcm260
1
vote
1
answer
236
views
1
answers
Comment: C: Help with NGS analysis
... Sounds like you could do with a collaborator. Where are you based? I'm sure there must be others at your institute that have experience with NGS. ...
written 5 days ago by mbyvcm260
1
vote
1
answer
126
views
1
answers
Answer: C: merging plink files
... The MAP line generated in the error looks like a PED line. Either your files (.map .ped) are named incorrectly, or you need to change the order you read them into PLINK. Your FID and IID should be alphanumeric. Removing the '-' may help? ...
written 6 days ago by mbyvcm260
1
vote
1
answer
160
views
1
answers
Answer: A: Converting Vcf File To Maf
... Try looking at [this post][1] [1]: https://www.biostars.org/p/74822/ ...
written 16 days ago by mbyvcm260
20
votes
4
answers
338
views
12 follow
4
answers
Forum: Bioinformatics in a clinical diagnostic setting versus research (academia)
... This question is primarily directed at next-generation sequencing pipelines/workflows, specifically aimed at variant discovery. I was wondering if there are any additional practices, quality control steps, that are implemented in a clinical diagnostic setting which are not routinely used by bioinfor ...
genome forum next-gen snp sequencing written 17 days ago by mbyvcm260 • updated 15 days ago by Keith Callenberg840
2
votes
1
answer
200
views
1
answers
Comment: C: how to Plot this figure with RNA-seq data using R?
... This is a volcano plot. Now you have a name for it you should be able to find plenty of code around, like [this][1]. [1]: http://www.gettinggeneticsdone.com/2014/05/r-volcano-plots-to-visualize-rnaseq-microarray.html ...
written 19 days ago by mbyvcm260
0
votes
0
answers
193
views
0
answers
Comment: C: Plink : how to filter outliers for GWAS ?
... If you are performing a single SNP analysis, generally it is not necessary to have the same number of samples for each variant. ...
written 6 weeks ago by mbyvcm260

Latest awards to mbyvcm

Scholar 4 days ago, created an answer that has been accepted. For C: merging plink files
Teacher 4 days ago, created an answer with at least 3 up-votes. For A: Is there a quick method to extract regularly-spaced features/SNPs from a VCF fil
Scholar 6 days ago, created an answer that has been accepted. For C: merging plink files

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1067 users visited in the last hour