I need to have a list of SNPs that are associated with diseases first.
people usually go to dbSNP http://www.ncbi.nlm.nih.gov/SNP/
but the UCSC snp138 table hg19 is much better accessible in terms of parsing.
See posts here: http://www.biostars.org/p/1288/
http://www.biostars.org/p/7073/
http://www.biostars.org/p/11701/
find SNPs associated with OMIM gene (by Pierre )
" Inspired by Khader's comment. The following mysql query for the mysql anonymous server at UCSC answers the SNPs in the OMIM genes:
mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -D hg18 -e '
select
concat(left(title1,30),"..."),
omimId,
S.name,
S.func,
G.chrom,
S.chromStart,
S.chromEnd
from
omimGene as G,
omimGeneMap as M,
snp130 as S
where
G.name=M.omimId and
G.chrom=S.chrom and
S.chromStart>=G.chromStart and
S.chromEnd <= G.chromEnd
limit 10;'
Result:
+-----------------------------------+--------+------------+--------------------+-------+------------+----------+
| concat(left(title1,30),"...") | omimId | name | func | chrom | chromStart | chromEnd |
+-----------------------------------+--------+------------+--------------------+-------+------------+----------+
| Nucleolar complex-associated p... | 610770 | rs72904505 | untranslated-3 | chr1 | 869480 | 869481 |
| Nucleolar complex-associated p... | 610770 | rs6605067 | untranslated-3 | chr1 | 869538 | 869539 |
| Nucleolar complex-associated p... | 610770 | rs2839 | untranslated-3 | chr1 | 869549 | 869550 |
| Nucleolar complex-associated p... | 610770 | rs3196153 | untranslated-3 | chr1 | 869586 | 869587 |
| Nucleolar complex-associated p... | 610770 | rs1133980 | untranslated-3 | chr1 | 869614 | 869615 |
| Nucleolar complex-associated p... | 610770 | rs28453979 | untranslated-3 | chr1 | 869781 | 869782 |
| Nucleolar complex-associated p... | 610770 | rs61551591 | intron,near-gene-3 | chr1 | 870079 | 870080 |
| Nucleolar complex-associated p... | 610770 | rs3748592 | intron,near-gene-3 | chr1 | 870100 | 870101 |
| Nucleolar complex-associated p... | 610770 | rs3748593 | intron,near-gene-3 | chr1 | 870252 | 870253 |
| Nucleolar complex-associated p... | 610770 | rs74047418 | missense | chr1 | 870364 | 870365 |
+-----------------------------------+--------+------------+--------------------+-------+------------+----------+instead you should do:
also by Pierre
1) Register an access to the FTP site of omim: http://omim.org/downloads and download mim2gene:
$ curl -s "ftp://anonymous:xxxxxxx@xxxxx.edu/OMIM/mim2gene.txt" | head
# Mim Number Type Gene IDs Approved Gene Symbols
100050 phenotype - -
100070 phenotype 100329167 -
100100 phenotype - -
100200 phenotype - -
100300 phenotype 100188340 -
100500 moved/removed - -
100600 phenotype - -
100640 gene 216 ALDH1A1
100650 gene/phenotype 217 ALDH2
get a list of the gene symbols:
~$ curl -s "ftp://anonymous:xxxxx@xxxxxx.edu/OMIM/mim2gene.txt" |\
egrep -v "#" | cut -d ' ' -f 4 | egrep -v '^\-$' |\
sort | uniq > list1.txt
2) get your list of SNP associiated to the gene symbol. Something like:
mysql -N --user=genome --host=genome-mysql.cse.ucsc.edu -A -D hg19 -e 'select distinct
G.geneSymbol,
S.name
from snp132 as S,
kgXref as G,
knownGene as K where
S.chrom=K.chrom and
S.chromStart>=K.txStart and
S.chromEnd<=K.txEnd and
K.name=G.kgId
/* AND something to restrict the result to YOUR list of SNPs or gene */
' | sort -t ' ' -k1,1 > list2.txt
3) use unix join to join the two lists:
join -1 1 -2 1 list1.txt list2.txt
you should get a list with two columns: the OMIM gene and your SNP.
I want to get a list of SNPs that are clinical associated. description of the snp138 table
http://genome.ucsc.edu/cgi-bin/hgTables
at terminal:
mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -D hg19 -e ' SELECT * FROM snp138 AS s WHERE s.bitfields LIKE "clin%" ' > clinic_associated_SNPs_hg19.txt
remember you are on the remote server of UCSC, you can not connect the database first, and do something like:
SELECT *
FROM snp138 AS s
WHERE s.bitfields LIKE "clin%"
INTO OUTFILE '/home/tommy/clinic_associated_SNPs_hg.txt'
FIELDS TERMINATED BY '\t'
LINES TERMINATED BY '\n';
Because we do not have the write privilege
after I got the txt file, I changed it to a bed file:
tommy@tommy-ThinkPad-T420:~$ cat clinic_associated_SNPs_hg19.txt | cut -f2-7 | head
chrom chromStart chromEnd name score strand
chr1 985954 985955 rs199476396 0 +
chr1 1199488 1199489 rs207460006 0 +
chr1 1245103 1245104 rs144003672 0 +
chr1 1265153 1265154 rs307355 0 +
chr1 1265459 1265460 rs35744813 0 -
chr1 1469330 1469331 rs145324009 0 +
chr1 1635334 1635335 rs201004006 0 +
chr1 1689555 1689556 rs207460007 0 +
chr1 1959074 1959075 rs121434580 0 +
tommy@tommy-ThinkPad-T420:~$ wc -l clinic_associated_SNPs_hg19.txt
103174 clinic_associated_SNPs_hg19.txt
There are total 103174 SNPs in the file.
Now, I can just use bedtools to intersect the SNPs bed file with the ChIP-seq bed file generated by MACS.
tommy@tommy-ThinkPad-T420:~$ bedtools intersect -a TF.bed -b SNPs_hg19.bed -wo
Just keep in mind the difference between the 0 based and 1 based coordinates system. See a post here:
Alternatively, you can create a database to do this kind of intersection by using Join command.
other tools
regulomeDB
http://regulome.stanford.edu/
a quick google
http://www.genomatix.de/online_help/help_gems/SNPInspector.html
http://viis.abdn.ac.uk/regsnp/Home.aspx
http://regulome.stanford.edu/
a quick google
http://www.genomatix.de/online_help/help_gems/SNPInspector.html
http://viis.abdn.ac.uk/regsnp/Home.aspx
Finally a python package for Database https://dataset.readthedocs.org/en/latest/quickstart.html
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