Hi, I am fairly new to bioinformatics and I was wondering if it was possible to achieve this is R. I have a fasta input file that contains a collection of 200 DNA sequences of the same length some of which have been mutated, the coordinates are provided in a sperate bed file. I also have a reference file with the sequence of chromosome 7 in it.
How do I align the reads to in the fasta file to the reference file and generate a report containing: gene name nature of the mutation (e.g. C->T etc) frequency of the mutation number of amplicons supporting the mutation reference sequence for the amplicon mutated sequence for the amplicon
Input files are available at the following link: https://drive.google.com/open?id=1lyKQ4e-ki24PBuV4iSsYPkVkamRDGxRK
Thank you for any help or insight
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