downloading dataset for snp analysis

Question

[jamessemaj712]

Hi,

I am new to Bioinformatics,I am from Computer Science background

I want to perform comparison of tools for snp. Therefore I need some raw data files. How do I get the data files? I searched a lot on internet but couldn't find a download button on any website which when clicked will give me the file in the proper format. Example I searched SRA, GEO, NCBI. But it is so confusing for the person who is a beginner in this field. Even my friend tried but in vain.

Please help

[iraun]

By "SNP analysis", you mean SNP calling analysis? Which type of file are you looking for? fastq format, fasta format, bam format?

[jamessemaj712]

Hi, Ya SNP calling analysis.I want in fasta format.

[iraun]

Well, SRA will give you all kind of datasets that you need. Using the ftp you will find the sequencing files from a wide range of organisms. Furthermore you'll find data becoming from all the sequencing plataforms, such as Illumina, 454 ... So you'll be able to find and download whatever you are interested in.

Here is the link: SRA

You'll need to convert .sra format to fastq (or fasta). To do that there is a nice easy tool called fastq-dump.

I forgot to mention. Here there is a nice tutorial covering this issue.

Answer 1

[GenoMax]

You could make synthetic datasets based on real genome sequence. You can get the human chromosomes here. Get *.fa.gz files.

[jamessemaj712]

Thank you very much.I think it is useful.At least I now know where to get the source file from.I will try it.