What program do I must to use to design primer for especific samples?

Question

[apl00028]

Hi, I'm trying to design primers for the most conservative region of my sequenced samples of CMV3. I would like design them according with my bowtie2 results (BAM File), which I got with my NGS data. What program do I must to use for my goal?

I'd appreciate any piece of information on this issue, thanks!!!!

Answer 1

[goodez]

NCBI's primer-blast is helpful https://www.ncbi.nlm.nih.gov/tools/primer-blast/. You can mostly just design them yourself and don't need to rely on software. Here's some general tips.

[apl00028]

yes, I am using this right now, but I would like to visualize them in my mapping view which I got in bowtie2

[goodez]

So is your question more about trying to identify these "most conserved regions" in your BAM file?

[Joe]

That’s not what bowtie2 is for...

[GenoMax]

apl00028 : You could use IGV with your alignments and the primers in a BED format file, if you want to view those together (after designing them with primer-blast as suggested).

[apl00028]

Finally I got the consensus sequence all my sequences and I found the primers in NCBI. I did not attempt import them to IGV in BED format because with the tool, find a motive, of IGV is enough to visualize them. Thanks for the answers.