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Old 03-16-2012, 02:45 AM   #1
fcr
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Question Programs to filter out the Mitochonrial DNA from Hightroughput Sequencing Reads

Hi all,

I have Whole Genome Shotgun Reads (Illumina) of a mammalian species. I am interested in filtering out all the reads matching mitochondrial DNA before starting the downstream analysis. I know the right thing is to blast them or map them against mtDNA. But, Do anyone knows about available software or scripts to do this? I would like to know if there are tools for it before writing the code myself.

Cheers,
Fernando
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Old 03-16-2012, 06:31 AM   #2
peromhc
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Although I have not tried this very approach, I bet you can use Bowtie combined with the --un feature.. Make a fasta file that contains your mt genome, build the bowtie index, and run.
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Old 03-16-2012, 12:16 PM   #3
swbarnes2
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Align to the whole genome, including mtDNA, using bowtie or bwa or whatever. Then you can filter your .bam for reads that align to the mtDNA.
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Old 03-16-2012, 07:21 PM   #4
husamia
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Quote:
Originally Posted by swbarnes2 View Post
Align to the whole genome, including mtDNA, using bowtie or bwa or whatever. Then you can filter your .bam for reads that align to the mtDNA.
I agree. there is no way to know which reads at mt so you have to align first.
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Old 03-17-2012, 12:35 AM   #5
mjp
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You could build indices with your mapping program of choice and map your reads to it.

Take a look at http://www.ncbi.nlm.nih.gov/genomes/...2759&hopt=html (Organelle Genome Resources) to download sequences for your indices.

Hope it helps.
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Old 03-17-2012, 04:08 AM   #6
SES
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Quote:
Originally Posted by fcr View Post
Hi all,

I have Whole Genome Shotgun Reads (Illumina) of a mammalian species. I am interested in filtering out all the reads matching mitochondrial DNA before starting the downstream analysis. I know the right thing is to blast them or map them against mtDNA. But, Do anyone knows about available software or scripts to do this? I would like to know if there are tools for it before writing the code myself.

Cheers,
Fernando
As a sanity check, be sure to BLAST the mtDNA against the genome after you have mapped or assembled your reads. The bowtie --un method is very fast for filtering reads, but unfortunately it does not work in my experience. Sure, it will filter out some reads but when you BLAST your assembly against the organelle genome after assembly it is quite clear that this type of filtering is not really effective.

It is slower, but I use BLAST for filtering, which leaves no contamination in the final assembly. Either way you choose to go, just keep in mind that checking that the filtering actually worked is quick and easy, and will reduce headaches downstream.
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