User: arronslacey

gravatar for arronslacey
arronslacey220
Reputation:
220
Status:
Trusted
Location:
United Kingdom
Last seen:
4 months ago
Joined:
4 years, 9 months ago
Email:
a**********@googlemail.com

about me

Posts by arronslacey

<prev • 79 results • page 1 of 8 • next >
3
votes
2
answers
232
views
2
answers
Convert SNPs from GrCh38 to 37
... The following SNPs are from the GRCh38 build 1 158766655 158766655 C T 1 162023402 162023402 T C 1 169793666 169793666 T G 1 6554475 6554475 G A 3 179604597 179604597 A C 4 39062542 39062542 A C 5 177089630 177089630 G A 8 142786489 142786489 C T 8 142879785 1428 ...
grch37 grch38 mapping snp written 4 months ago by arronslacey220 • updated 4 months ago by harold.smith.tarheel4.0k
0
votes
1
answer
323
views
1
answers
Comment: C: merging humsavar dataset with UniprotKB human variation
... Hi @emmahe - Although the chromosome number and chromosome position are given in the annotation track bed file, the nucleotide allele change is not present. I perhaps should have explained this a bit better. Thanks. ...
written 4 months ago by arronslacey220
0
votes
1
answer
323
views
1
answer
merging humsavar dataset with UniprotKB human variation
... Hi - in the current release ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/variants I am interested in putting all variants annotated within humsavar.txt through Annovar or other annotation tools. Perhaps even score them with something like CADD. I require all the varian ...
ensembl swissprot uniprot snp annovar written 5 months ago by arronslacey220 • updated 5 months ago by emmahe40
1
vote
1
answer
518
views
1
answer
drug response variant datasets
... Hi - I am looking for sources of drug response data at SNP level for data mining purposes in my Phd. I m aware of Biobase's PGMD which looks promising, however I don't have the 12k euros for the download subscription for raw access! I'd be very grateful of anyone knows of any alternative databases. ...
snp variant drug response biobase written 16 months ago by arronslacey220 • updated 14 months ago by dyollluap300
0
votes
1
answer
539
views
1
answers
Comment: C: chromosomal locations of snps in humvar variant set
... Thanks Elisabeth - very helpful! I had also looked into the Bisoconductor package VariantAnnotation that includes data objects such as polyPhen.Hsapiens.dbSNP131 - which maps most of the rsids to the humsavar dataset. it's obviously a bit out of date now so I much appreciate alternative data scourse ...
written 21 months ago by arronslacey220
2
votes
1
answer
539
views
1
answer
chromosomal locations of snps in humvar variant set
... Hi - in the humsavar dataset there are variants given by protein position and amino acid change. http://www.uniprot.org/docs/humsavar Is there a way to convert these to chromosome positions and nucleotide changes? thanks. I should probably add for clarification that some snps listed to do not hav ...
variation humvar snp uniprot written 21 months ago by arronslacey220 • updated 21 months ago by Elisabeth Gasteiger1.3k
2
votes
1
answer
821
views
1
answer
how can I obtain benign / neutral snps?
... Hi everyone - using the UCSC server it seems I can obtain disease causing SNPs from snp144 by doing something like select * from snp144 where bitfields like '%has-omim-omia%' but I would like to know if there is a preferred way to select non-disease causing snps. i.e. known to be benign. Is th ...
annovar dbnfsp snp mysql dbsnp written 21 months ago by arronslacey220 • updated 21 months ago by WouterDeCoster25k
0
votes
1
answer
953
views
1
answers
Comment: C: Multiple annotations using annovar?
... just one thing - table_annovar.pl does not seem to preserve additional custom fields specified in the input file, where annotate_variation.pl appears to do this. do you happen to know how to keep extra columns in the input? all my additional columns are in the format comments: field1 field ...
written 22 months ago by arronslacey220
0
votes
1
answer
953
views
1
answers
Comment: C: Multiple annotations using annovar?
... excellent thanks very much! ...
written 22 months ago by arronslacey220
3
votes
1
answer
953
views
1
answer
Multiple annotations using annovar?
... Hi - is it possible to add multiple annotations in the same command with annovar. For example annotation with both exac and 1000g? The command for one is this: perl annotate_variation.pl -filter -build hg19 -dbtype exac03 GLRA1.txt humandb/ so I have tried perl annotate_variation.pl -f ...
annovar variant annotation written 22 months ago by arronslacey220 • updated 22 months ago by igor5.0k

Latest awards to arronslacey

Great Question 16 months ago, created a question with more than 5,000 views. For BLAST Database error: No alias or index file found for nucleotide database
Great Question 16 months ago, created a question with more than 5,000 views. For Trying To Run Psipred But Failing To Use Blastpgp
Epic Question 16 months ago, created a question with more than 10,000 views. For BLAST Database error: No alias or index file found for nucleotide database
Popular Question 16 months ago, created a question with more than 1,000 views. For get protein sequence from ID
Popular Question 16 months ago, created a question with more than 1,000 views. For SIFT ncbi executables setup incorrectly?
Popular Question 16 months ago, created a question with more than 1,000 views. For Anyone Use R For Their Bioinformatics Work?
Popular Question 16 months ago, created a question with more than 1,000 views. For BLAST Database error: No alias or index file found for nucleotide database
Popular Question 16 months ago, created a question with more than 1,000 views. For How Long Does Running Psipred Take ~ 600 Sequences In A Fasta File
Popular Question 19 months ago, created a question with more than 1,000 views. For Protein Hmm Profile In R/Python?
Popular Question 19 months ago, created a question with more than 1,000 views. For Pyfasta Split By Header
Popular Question 20 months ago, created a question with more than 1,000 views. For Anyone Use R For Their Bioinformatics Work?
Popular Question 23 months ago, created a question with more than 1,000 views. For Pyfasta Split By Header
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Pyfasta Split By Header
Great Question 2.2 years ago, created a question with more than 5,000 views. For BLAST Database error: No alias or index file found for nucleotide database
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Pyfasta Split By Header
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Run Multiple Sequences Through Psipred
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Query Genbank Using A Mysql Interface
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Anyone Use R For Their Bioinformatics Work?
Popular Question 3.1 years ago, created a question with more than 1,000 views. For BLAST Database error: No alias or index file found for nucleotide database
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Run Multiple Sequences Through Psipred
Popular Question 3.4 years ago, created a question with more than 1,000 views. For Anyone Use R For Their Bioinformatics Work?
Supporter 3.5 years ago, voted at least 25 times.
Popular Question 3.9 years ago, created a question with more than 1,000 views. For Trying To Run Psipred But Failing To Use Blastpgp

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1756 users visited in the last hour