Hello everyone
i have questions please
my data is contaminated by host mitochondrial DNA , and i need to do mapping of my data against host mitochondrial DNA and extract unmapped reads to do assembly next
first : how can i download just mitochondrial DNA and not the entire genome of the host speceis ? second , can anyone please tell me the blast command i should use ? third : how can i obtain unmapped reads ?
really do need your help and Thank you so much .
1 answer
You can extract mitochondrial genomes by trying a search such as this one at NCBI. Here is an example of Fly or Mouse searches. Replace your organism name and see if you can get the sequence.
You can't extract unmapped reads by using blast. If you have fastq data then using bbsplit.sh from BBMap suite to bin your data to separate mitochondrial reads would be your best option. Find BBsplit in this guide by searching. Once you do that your unmapped reads should be in a file.
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