Question: What program do I must to use to design primer for especific samples?
0
gravatar for apl00028
2.1 years ago by
apl0002870
apl0002870 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 • 455 views
ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by apl0002870
1
gravatar for goodez
2.1 years ago by
goodez480
United States
goodez480 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 2.1 years ago by goodez480

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 2.1 years ago by apl0002870

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

ADD REPLYlink written 2.1 years ago by goodez480

That’s not what bowtie2 is for...

ADD REPLYlink written 2.1 years ago by Joe17k

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 2.1 years ago • written 2.1 years ago by genomax87k

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 2.1 years ago by apl0002870
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1373 users visited in the last hour