User: rdlady

gravatar for rdlady
rdlady40
Reputation:
40
Status:
New User
Location:
Last seen:
1 year, 7 months ago
Joined:
3 years, 8 months ago
Email:
r*****@gmail.com

Posts by rdlady

<prev • 16 results • page 1 of 2 • next >
1
vote
0
answers
1.0k
views
0
answers
Comment: C: CrossMap liftover: REF alleles in VCF files overwritten by reference genome file
... If Crossmap expects us to have already fixed the REF alleles, why it tries to fix swaps/flips instead of reporting an error, or just ignoring them (like liftover tool)? What I'm saying is that Crossmap should either remove this REF allele "fix" function that creates artifacts, or do the fix correctl ...
written 19 months ago by rdlady40
0
votes
1
answer
4.2k
views
1
answers
Comment: C: Question: Is there a way to reformat vcf 4.3 down to 4.2?
... The sed command you suggested worked for the analyses I needed. Thank you again for your help! ...
written 2.0 years ago by rdlady40
0
votes
1
answer
4.2k
views
1
answers
Comment: C: Question: Is there a way to reformat vcf 4.3 down to 4.2?
... That's a good idea. I was concerned that v4.3 might be too different from 4.2 but you are right, I should at least just try to change the version number in the vcf file and see if that works. Thank you! I will post an update if that works. ...
written 2.0 years ago by rdlady40
6
votes
1
answer
4.2k
views
1
answer
Question: Is there a way to reformat vcf 4.3 down to 4.2?
... I got a vcf file from the supplementary materials of an article but the vcf file is in vcf 4.3 format. Is there a way to convert the vcf from 4.3 to 4.2 format? ...
chip-seq snp sequencing written 2.0 years ago by rdlady40 • updated 2.0 years ago by Pierre Lindenbaum129k
1
vote
0
answers
972
views
0
answers
Is there a database with information on percent spliced in (PSI) fraction for a gene?
... I have a quick question. Is there any databases with information on the percent spliced in (PSI) fraction of a given gene? I was wondering is this kind of experimental data is stored in any database. It would be great if I could use an Ensenbl gene ID as input, for example, and get the PSI score ...
gene genome splicing transcription written 3.5 years ago by rdlady40
3
votes
2
answers
1.4k
views
2
answers
Answer: A: retrieve complete gene sequence (exons and introns) from SNP name (rsid)
... I think I got it!!!!! R's biomaRt library is amazing! I was able to retrieve the complete gene sequences (introns+exons) for the gene where my SNP is located. I made an R script that retrieves the complete gene sequence and its variations using a SNP name or rsid as input. The script is available ...
written 3.5 years ago by rdlady40
0
votes
2
answers
1.4k
views
2
answers
Comment: C: retrieve complete gene sequence (exons and introns) from SNP name (rsid)
... Oh I see it. Thanks! But I still couldn't find a way to automatically download the complete ORF using these queries. ...
written 3.5 years ago by rdlady40
0
votes
2
answers
1.4k
views
2
answers
Comment: C: retrieve complete gene sequence (exons and introns) from SNP name (rsid)
... I mean the unspliced gene sequences (intros+exons). I found the biomaRt R package that seems to do what I want, but I'm learning about it yet. I will share the info here if biomaRt is able to extract the complete ORF/gene. ...
written 3.5 years ago by rdlady40
0
votes
2
answers
1.4k
views
2
answers
Comment: C: retrieve complete gene sequence (exons and introns) from SNP name (rsid)
... Thanks for your reply! Sorry maybe I didn't expained myself well in my example: I want the COMPLETE GENE sequence, including introns and exons, not the Xbp flanking sequence. And I want an automatic method, not a website that I have to click, because I will have to retrieve this info for more than 1 ...
written 3.5 years ago by rdlady40
0
votes
2
answers
1.4k
views
2
answers
Comment: C: retrieve complete gene sequence (exons and introns) from SNP name (rsid)
... Thanks for answering, but in the dbSNP I can't find the complete gene sequence (introns and exons included) of the gene belonging to the SNPs. Where exactly do you click to find that? ...
written 3.5 years ago by rdlady40

Latest awards to rdlady

Popular Question 23 months ago, created a question with more than 1,000 views. For Importing SNP and phenotype data from dbGaP into R
Scholar 3.5 years ago, created an answer that has been accepted. For A: retrieve complete gene sequence (exons and introns) from SNP name (rsid)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 713 users visited in the last hour