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Old 05-24-2013, 04:47 AM   #1
vishalthapar
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Location: NY

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Default Align reads to 1 gene

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
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Old 05-24-2013, 06:48 AM   #2
lkral
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Geneious works very well for this. You just select the gene sequence and the list of reads and use the map to reference function.
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Old 05-24-2013, 07:34 AM   #3
chadn737
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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.
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