Question: Sheep Genome and Chromosome
0
gravatar for hosein_salehi6
6 months ago by
hosein_salehi60 wrote:

I have some coordinates from sheep chromosomes like : chr24:40902129-41709809 chr25:11035146-11097889 chr26:10400726-10968027 , How I can find genes in this coordinates by the fastest and newest db and methods . Please help me .Thanks.

genome • 196 views
ADD COMMENTlink modified 6 months ago by Pierre Lindenbaum115k • written 6 months ago by hosein_salehi60
2
gravatar for genomax
6 months ago by
genomax59k
United States
genomax59k wrote:

Use Ensembl BioMart.

Ensembl Genes --> Sheep Gene v.3.1(hope you have the latest build) --> Filters (left column) --> Multiple Regions --> Paste in your intervals (500 at one time max, remove prefix chr from intervals) --> Attributes (left column) --> Gene --> select Gene Name --> Click on count(top left of page) --> Results.

ADD COMMENTlink written 6 months ago by genomax59k

Thank you. But unfortunatly I have V4.0 version

ADD REPLYlink written 5 months ago by hosein_salehi60
0
gravatar for WouterDeCoster
6 months ago by
Belgium
WouterDeCoster35k wrote:

Download a bed file from the UCSC table browser and use bedtools

ADD COMMENTlink written 6 months ago by WouterDeCoster35k
0
gravatar for Pierre Lindenbaum
6 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum115k wrote:

using mysql/ucsc

$ echo -e "chr19:50686000-50700183\nchr24:40902129-41709809\nchr25:11035146-11097889" |\
  awk -F '[:-]' 'BEGIN{printf("select * from refGene where ");} {printf("%s (chrom=\"%s\" and NOT(txEnd<%d OR txStart>%d)) ",(NR==1?"":" OR "),$1,$2,$3);} END {printf(";\n");}'  | \
 mysql --user=genome --host=genome-mysql.soe.ucsc.edu -A -P 3306 -D oviAri3  -t
+-----+--------------+-------+--------+----------+----------+----------+----------+-----------+--------------------------------------+--------------------------------------+-------+-------+--------------+------------+------------+
| bin | name         | chrom | strand | txStart  | txEnd    | cdsStart | cdsEnd   | exonCount | exonStarts                           | exonEnds                             | score | name2 | cdsStartStat | cdsEndStat | exonFrames |
+-----+--------------+-------+--------+----------+----------+----------+----------+-----------+--------------------------------------+--------------------------------------+-------+-------+--------------+------------+------------+
| 971 | NM_001161875 | chr19 | +      | 50686975 | 50696070 | 50686975 | 50696070 |         4 | 50686975,50691449,50695264,50695896, | 50687131,50691570,50695395,50696070, |     0 | RHOA  | cmpl         | cmpl       | 0,0,1,0,   |
+-----+--------------+-------+--------+----------+----------+----------+----------+-----------+--------------------------------------+--------------------------------------+-------+-------+--------------+------------+------------+
ADD COMMENTlink modified 6 months ago • written 6 months ago by Pierre Lindenbaum115k
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