Mapping digested synthetic oligos back to original sequences.
I have several synthetic dsDNA of 70bp and I digest them with some enzyme. I am interested to see the exact cut site of the enzyme so I had the products sequenced using MiSeq. They are single-end read. What is the best way to see the reads profile relative to the original dsDNA sequences?
I created an artificial reference file of the original sequences (using only one strand) and then tried to map the sequences which are relatively short (19 – 50 bp) to the reference using bowtie2 and bwa. Then I viewed them in IGV browser but the outcome is not what I expected. A lot of reads that I see by just eye rolling fastq file or greping do not appear in IGV. I am not sure if I can use different aligners that are performing better for this scenario. What do you recommend? Let me know what other information makes the situation more clear. Thanks!
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