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Old 08-17-2016, 11:04 PM   #6
tristan dubos
Location: France

Join Date: Dec 2015
Posts: 39

You can do it with bwa (it s an aligner) who will map your sequencing illumina against your references . You need to modify your references genes with N before and after ( N is considering as any nucleotide ) and in the bwa a parameter you need to permit mismatch on this N. You have to care about the minimum number of match you consider at the border of your sequences to be sure of the identity of you sequences. That the way to define the number of N considering the length of you reads from the sequencing.
Then you will looked at the sequences who mapped on the N. To extract this sequences i don t really know tools it more bio-informatics code ...
I will looked how to make a consensus for this part it may be a easier way .

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