I have .fastq files from a targeted amplicon seq run on MiSeq using Illumina library prep workflow. How do I process it so that I get the targeted sequences? What is the pipeline to use for processing amplicon sequencing?thanks in advance.
Based on amplicon size, you may either map the paired-end reads or generate the combined reads (from the pairs) before mapping to the reference genome. It should be straightforward with BWA (or BWA MEM). How you deal with the alignments largely depends on the purpose of the experiment, genotyping or sequence assembly, could all start from the BAM files.