I have analysed my NGS data from Illumina (RRBS), I have fragments of information (chromosome, genomic position etc) and I would like to search against databases and see whether there are any common SNPs present in my fragments. I presume I would find DbSNPs (131 or 135 may be), but if anyone details the process or can give me advice which will enable me to do this search quickly that will be much appreciated.
Have you tried using GALAXY to align your fragments to DbSNP? What exactly are you trying to do?
I think a simple perl code will serve the purpose, if I understood your problem correctly..
In case you have variant information (chromosome, genomic position) use annovar, which is quite simple to use and provide nice filtering options
Thanks guys.. but Galaxy would handle the volume of data I have... it freezes..
Back to the blackboard.. say I have a fragment ( I didnt RRBS, methylation analysis by restriction fragments)..
and have information like this
Chr postition fragment lenth
1 1423332- 1423398 68
2 1123301- 1123399 98
..................... and so on
and have 30000 fragment like this.
I want to do a small analyis and see whether this fragments which I got from my methylation analysis can contain any known known SNPS in them ( searching against databases, say with a frequency of >1% in population).
also, If I want to look presence of common SNPS in + and -100 bp of the fragments. I.e.- in a lenth of 268 base and 298 base for the above fragments.
Any suggestions please.
In case your not so familar with programming or setting up annovar, you can use the http://www.snp-nexus.org/ website. The only drawback is the dbsnp build 132, the current release is 137
- Badges
- Science method