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Old 09-17-2015, 10:35 PM   #1
ktayal
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Default Selective assembly of Genome

I am interested in assembling a part of the genome, not the whole genome . I have the read file for the whole genome. Is there any possible way by which i can get a subset of reads for the part of the genome that i am interested in and then i can apply assembly over that subset of reads.

I am newbie to this field . Can you point me out to the literature where people have done this thing.
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Old 09-17-2015, 10:52 PM   #2
macarima
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No. You can't select a part of genome.
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Old 09-18-2015, 02:06 AM   #3
v_kisand
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if you have a good enough reference genome, map all reads with low stringency to reference and filter out region of interest. Only it is hard to see the scientific idea behind this...
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Old 09-18-2015, 12:53 PM   #4
gringer
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Well, sure, as long as you know the sequence for the region you want to assemble. Just map the reads to that sequence, then redirect all mapped reads to another output file. HISAT2 has options '--al' and '--al-conc' to do this.
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