Question: Ucsc Dbsnp131 Table Format
2
gravatar for Biomed
9.8 years ago by
Biomed4.6k
Bethesda, MD, USA
Biomed4.6k wrote:

Hi, I want to create a bed file that contains leftflank-rightflank positions of a subset of dbsnp131 table I downloaded from UCSC. The problem is when I look at the data there are two fileds chromStart and ChromEnd but in most cases that I saw these were sequencial numbers like Chr1 134567 134568 .So what do those chrStart and chromEnd positions exactly mean and how can I get a leftflank-right flank position data for the snps that I am interested in? Thanks

mysql> select * from snp131 limit 10;

bin | chrom | chromStart | chromEnd | name| score | strand | refNCBI | refUCSC | observed | molType

| 585 | chr1 | 10433 | 10433 | rs56289060 | 0 | + | - | - | -/C | genomic | insertion | unknown | 0 | 0 | near-gene-5 | between | 1 |

| 585 | chr1 | 10491 | 10492 | rs55998931 | 0 | + | C | C | C/T | genomic | single | unknown | 0 | 0 | near-gene-5 | exact | 1 |

| 585 | chr1 | 10518 | 10519 | rs62636508 | 0 | + | G | G | C/G | genomic | single | unknown | 0 | 0 | near-gene-5 | exact | 1 |

bed dbsnp ucsc • 2.4k views
ADD COMMENTlink modified 9.4 years ago by Stephane Plaisance410 • written 9.8 years ago by Biomed4.6k
6
gravatar for Pierre Lindenbaum
9.8 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum128k wrote:

It is an half-open interval.

chromStart: is the starting position ( 0-based) of the SNP on the chromosome

chromEnd: is the position where there is NO MORE snp.

so chromEnd-chromStart = length of the variation. e.g. if length=0, the SNP is a deletion

ADD COMMENTlink modified 9 months ago by RamRS27k • written 9.8 years ago by Pierre Lindenbaum128k

SO for a Single nucleotide variation chromstart is actually where the variation occures and the leftflank would be chromstart-1 while the rightflank would be chromEnd, right?

ADD REPLYlink written 9.8 years ago by Biomed4.6k

@biomed yes

ADD REPLYlink written 9.8 years ago by Pierre Lindenbaum128k
3
gravatar for Stephane Plaisance
9.8 years ago by
Leuven area (Belgium)
Stephane Plaisance410 wrote:

and

BedTools has commands to retreive (boundary) sequences from the fasta ref genome and a BED file

the current SNP track first need be processed to add few bases each side using yet another bed tool. Then you get the fasta sequences with fastaFromBed

have a look to the version v2.9.0 manual about the command details slopBed (get bordering bases) fastaFromBed (extract resulting sequences)

I love BedTools !

Cheers, Stephane, BITS-VIB

ADD COMMENTlink written 9.8 years ago by Stephane Plaisance410
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1129 users visited in the last hour