Question: processing amplicon seq data from miseq
gravatar for sc222
6 days ago by
sc2220 wrote:

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.

next-gen • 127 views
ADD COMMENTlink modified 5 days ago by Vitis1.7k • written 6 days ago by sc2220

FYI: This is crossposted on stackexchange.

ADD REPLYlink written 5 days ago by finswimmer8.8k
gravatar for Vitis
5 days ago by
New York
Vitis1.7k wrote:

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.

ADD COMMENTlink written 5 days ago by Vitis1.7k
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