Align reads to 1 gene

[vishalthapar]

Hi All,

I need to align ABI Solid reads to just 1 gene to see how many reads align to just that gene. (No mapping has been done so far). I need to know what is the best way to do this. It seems like an over kill for me to create a reference file, index etc for 1 gene and then align the read files using any aligner (I am leaning towards NovoalignCS but other suggestions with reasons are welcome). Is there a simpler method to do this kind of single gene alignment for reads?

Thanks,

Vishal

[lkral]

Geneious works very well for this. You just select the gene sequence and the list of reads and use the map to reference function.

[chadn737]

Depending on how you did your experiment, be cautious in mapping to a single gene.

If you sequenced an entire genome/transcriptome and map this only to a single gene, then reads that should map to other locations may end up being incorrectly being mapped to that gene, inflating the number of reads mapping to it.