Exome reference sequence

[nisha]

Hi all,

I have to map Solexa exonic reads for which I need the human exome reference sequence. Could someone please tell me where I could download/ftp a copy of the exome?

Thanks,
N

[bioinfosm]

Hi,

Did you get some information on that? Perhaps its the whole human genome one can use for exome data mapping.

Any particular tools you found to work better for exome analysis?

Also, is there a way to annotate the SNP events found after mapping, provide information like codon change, which exon of what gene, etc.?

thanks,

[NextGenSeq]

For assembly of exome data we find it's best to use the reference genome. This is because with exome enrichment you get ~50 to 100 bp of flanking intron sequence. Thus you can detect splice mutations if you assemble against the genome.

http://hgdownload.cse.ucsc.edu/downloads.html

If for some reason you don't want to do this you can download the entire refseq database for your organism of interest.

http://www.ncbi.nlm.nih.gov/RefSeq/

[bioinfosm]

Yeah, moreover am looking at the bed file of capture region. Prob worth a try to generate a bed mapping file and try using the bedtools to get % coverage, exons seqeunced, etc information

[blackgore]

Not the same analysis, I know, but the way this thread is phrased, I saw (hallucinated?) some similarity between exome mapping and the alignment stage of an rna-seq experiment. To that end, could similar software be used, i.e. feeding the exome reads into TopHat? I've not tried running TopHat without including a GFF file before, but another post on here ( http://seqanswers.com/forums/showthread.php?t=1626 ), which I hope I interpret correctly, suggested that without it, the program could generate an 'islands' bed file ("islands" ~ "exons")

[bioinfosm]

I would be curious if someone used tophat in that way! Bedtools worked nicely so far, using the expected capture dataand finding on-target stuff and coverage