Degenerate primers
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20 days ago
M1985 • 0

Hi Im not very familiar with ngs data. I want to know if i did pcr with primers that i dont know the sequence can i use alignments of sequences from ngs data before trimming to find from what locations my pcr was done?

Thanks

Trimming • 451 views
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20 days ago
JC 13k

Yes, you can, also you can use FastQC to detect which primers were used.

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Can you please help me on this? Any chance I could email you the data? I don't have access to the software or have any experience in what tools to use. Also this data is from a minion device

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Do not add answers unless you're answering the top level question. Use Add Comment or Add Reply instead as appropriate. I'll merge and move your posts to the right location this time, but please be more careful in the future.

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20 days ago
GenoMax 139k

Also this data is from a minion device

Since we don't fully know what you are trying to do (or what your construct is supposed to look like) this may be a bit difficult to answer.

can i use alignments of sequences from ngs data before trimming to find from what locations my pcr was done?

That is what you may need to do. What is the size of the amplified product? Since not all nanopore reads will be full length you may need to work on manually editing the alignments. Hope you have a reference available, which will make this a little easier.

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Yes this from the HLA region. The size of the amplicons are from 1kb-4kb. Can I contact you via email?

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Please do not ask to take the conversation off the forum.

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