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

Join Date: Mar 2009
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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?


vishalthapar is offline   Reply With Quote
Old 05-24-2013, 06:48 AM   #2
Location: Carrollton, GA

Join Date: May 2011
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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.
lkral is offline   Reply With Quote
Old 05-24-2013, 07:34 AM   #3
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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.
chadn737 is offline   Reply With Quote

abi solid, alignment, count, single gene

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