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You might say I'm an amateur bioinformatician, or trying to become one. I have a BAM file, from which I have succeeded, using UGENE , in extracting consensus data in FASTA format. I now see a single series of nucleotides, and their complements, for each chromosome. What I don't see is two corresponding sequences. SNP data (e.g., SNPedia ) cites (if I understand it correctly) the SNP at the same site on each chromosome in the pair. I don't know how to determine my variation, since I see only one nucleotide at any given site, not the pair.

Pretty sure I'm missing something fundamental here. Thanks for any help navigating this jungle!

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  • $\begingroup$ "Two corresponding sequences": corresponding to what? What SNP data? What SNP should be on both chromosomes? The link you gave seems to be for a SNP that can be either hetero- or homozygous. Why are you assuming it is homozygous in your data? What are your data? Please edit your question and clarify, it is very hard to understand what you're asking at the moment. $\endgroup$ – terdon Nov 22 '15 at 16:48
  • $\begingroup$ Sorry if I'm not expressing myself well... I'm kinda new to all this. I am, in effect, talking about what I should expect to see in the case of a heterozygous SNP. The question is simply this: If the particular genome I am examining happens to have a heterozygous SNP at some site, let's say (C;T), then how/where would I expect to see this in my data? A consensus reflects the more prevalent read at that site, but, in this case, I would expect about 50% of the reads to be C, and 50% T... so the consensus isn't useful. Am I wrong? $\endgroup$ – Marc Nov 22 '15 at 18:26
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If you are looking for simple one off queries it might be better to load the BAM file and a relevant reference genome into a browser like IGV and simply navigate to that specific position.

For some data I had lying around a heterozygous SNP would look like the picture below, there has been an A to G SNP and a C to T:

For longer lists of queries I would take a look at BEDtools: https://bedtools.readthedocs.org/en/latest/content/bedtools-suite.html

If this does not help you, I recommend you ask your question on https://www.biostars.org/ There you will find help from true bioinformaticians.

enter image description here

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  • $\begingroup$ Right, so I've been looking at the BAM file, but I've yet to find any instance of a site where I see 50/50 reads of two nucleotides (e.g. 50% C and 50% T). Is this what I should expect to find in the case of a heterozygous SNP genotype? If so, then should I just ignore the consensus and just look at the BAM file? I'd just like to validate that I am on the right track here... $\endgroup$ – Marc Nov 22 '15 at 18:30
  • $\begingroup$ I adjusted the answer to include a picture. Hopefully everything is more clear now $\endgroup$ – mimat Nov 23 '15 at 12:41
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I wouldn't necessarily expect regions of heterozygosity to be apparent from a consensus fasta. I'd eyeball if you know some potential sites, or run your .bam through something that will call SNPs.

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