Dear all,
I have been sequencing some samples and found something that is new for me.
After sequencing using Miseq, I usually align reads using CLC Genomic Workbench and from there, I get the visual of the mapping in general before proceeding to any downstream analysis.
Now, I've got some area of zero coverage and immediately though of sequencing errors. The problem is that this "hypothetical" error is seen in all my samples at a particular gene that is not seen by PCR in 1/2 of my samples (so it was reported as missing in PCR experimental data for those samples).
So, finally this let me think about just a kind of large deletion in the gene that has caused a significant change (for it not to be amplified by PCR) and altered presumably the function of of it. Does it make sense?
I think a gene may not be amplified in PCR for a number of reasons (no need to list them here), and obviously, sanger sequencing can not help. But for NGS, what should we expect? Please help brainstorming about this and see if I can come up with a new idea from the forum.
Please see attached the visualization of the mapping at that region (2 samples).
Thanks all,
I have been sequencing some samples and found something that is new for me.
After sequencing using Miseq, I usually align reads using CLC Genomic Workbench and from there, I get the visual of the mapping in general before proceeding to any downstream analysis.
Now, I've got some area of zero coverage and immediately though of sequencing errors. The problem is that this "hypothetical" error is seen in all my samples at a particular gene that is not seen by PCR in 1/2 of my samples (so it was reported as missing in PCR experimental data for those samples).
So, finally this let me think about just a kind of large deletion in the gene that has caused a significant change (for it not to be amplified by PCR) and altered presumably the function of of it. Does it make sense?
I think a gene may not be amplified in PCR for a number of reasons (no need to list them here), and obviously, sanger sequencing can not help. But for NGS, what should we expect? Please help brainstorming about this and see if I can come up with a new idea from the forum.
Please see attached the visualization of the mapping at that region (2 samples).
Thanks all,
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