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
Yes, you can, also you can use FastQC to detect which primers were used.
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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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
Do not add answers unless you're answering the top level question. Use
Add CommentorAdd Replyinstead as appropriate. I'll merge and move your posts to the right location this time, but please be more careful in the future.