Question: What program do I must to use to design primer for especific samples?
0
gravatar for apl00028
10 months ago by
apl000280
apl000280 wrote:

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!!!!

primer alignment genome • 291 views
ADD COMMENTlink modified 10 months ago • written 10 months ago by apl000280
1
gravatar for goodez
10 months ago by
goodez460
United States
goodez460 wrote:

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.

ADD COMMENTlink written 10 months ago by goodez460

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

ADD REPLYlink written 10 months ago by apl000280

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

ADD REPLYlink written 10 months ago by goodez460

That’s not what bowtie2 is for...

ADD REPLYlink written 10 months ago by jrj.healey11k

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).

ADD REPLYlink modified 10 months ago • written 10 months ago by genomax65k

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.

ADD REPLYlink written 9 months ago by apl000280
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