Hello,
I ran 48 samples from museum specimens on the MiSeq platform. Unfortunately, each sample has very low coverage (~0.0035x). One of the contributing factors appears to be that the average read size is 38 bp, which may be due to the large amount of sheering present in museum samples.
I was able to extract ~60 SNPs, but cannot produce any supported trees or STRUCTURE results. I know the low coverage is to blame, but I am not sure the minimum coverage that would be usable for an analysis. I typically see papers use coverages of >5x. Papers with lower coverage (the lowest I have seen is 0.5x typically mention that they would like to acquire further coverage).
However, to get that amount of coverage for one sample would require an entire lane of the HiSeq platform, which would provide 30x coverage than the MiSeq. If I went for 0.5x coverage, I could run 10 samples.
Is there a hard rule suggesting the minimum amount of coverage for a phylogenetic analysis? Is running these samples on a HiSeq worth the cost?
EDIT: I do have a reference genome for my species.
I ran 48 samples from museum specimens on the MiSeq platform. Unfortunately, each sample has very low coverage (~0.0035x). One of the contributing factors appears to be that the average read size is 38 bp, which may be due to the large amount of sheering present in museum samples.
I was able to extract ~60 SNPs, but cannot produce any supported trees or STRUCTURE results. I know the low coverage is to blame, but I am not sure the minimum coverage that would be usable for an analysis. I typically see papers use coverages of >5x. Papers with lower coverage (the lowest I have seen is 0.5x typically mention that they would like to acquire further coverage).
However, to get that amount of coverage for one sample would require an entire lane of the HiSeq platform, which would provide 30x coverage than the MiSeq. If I went for 0.5x coverage, I could run 10 samples.
Is there a hard rule suggesting the minimum amount of coverage for a phylogenetic analysis? Is running these samples on a HiSeq worth the cost?
EDIT: I do have a reference genome for my species.
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