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Old 12-19-2014, 04:12 AM   #3
JenBarb
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Location: Bethesda, MD

Join Date: Oct 2010
Posts: 47
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Hi Brian,
Yes basically, I am involved with a metagenomics study where I have 200-250bp sequence reads from Next Gen Sequencing derived from different regions of the 16s gene, i.e. 6 different primers (primer sequences are unknown as they are from a commercial kit and the company informed us that they are proprietary). For example, one fastq file that I have contains ~170K reads all from different regions of the 16s gene. I would like to be able to blast my reads against a database of bacteria so that in return I get each read aligned to the 16s gene somewhere and it's genomic coordinate, there I will know where a read in my file is derived form within the gene.

Does this make sense? The HOMD database (www.homd.org) allows one to blast a total of only 3000 reads. I am looking for a different tool that will allow me to blast all of my reads and will return the alignments, and percent identity along with where the read aligned along the gene.

Jen
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