How Do I Get The Reads That Correspond To A Particular Gene Of Interest

Question

[Sandy]

I want to know how to get short read of a particular "gene" of interest. For example if I want to get reads of VCL how and where to find it?

I want to download short reads of the gene VCL. how to do it?

[Michael]

Try to be more specific. Tell us precisely what data you have and what you tried. Your question could be interpreted in many ways and I'm not going to guess what you really want.

[Michael Schubert]

Most importantly, do you want traces or inferred sequences?

Answer 1

[lh3]

Get your gene coordinate and for example:

samtools view -b ftp://ftp.ncbi.nih.gov/1000genomes/ftp/data/HG00096/alignment/HG00096.chrom20.ILLUMINA.bwa.GBR.low_coverage.20101123.bam chr:start-end > HG00096.VCL.bam

There are alignment data for >1000 human individuals.

Answer 2

[Michael]

The sequence read archive is still online. Afaik, there is no service that allows to get the reads only for a single gene, this is quite a good decision not to let you have this option, given the whole raw data archive is over 1 Pb in size! The alignment information, not to mention the gene annotations single reads fall into, is not even stored, and it might not even be possible to do so.

Instead download some reads, after you know what kind of data you want and align them yourself against the gene sequence or whole human chromosome 22. The user interface of SRA is terrible btw, so you will need some time to figure out where to go or just do a search for all human sequences like here and browse the available data.

Answer 3

[Michael Schubert]

The European Nucleotide Archive supports searching for entries and VCL yields 2 entries for which there is additional sequencing information available, one from human and one from mouse:

• CH466613
• CH471083

However, all I could find were contings and no reads - maybe they're in there somewhere, I didn't check too thoroughly.