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when I convert hg19 to hg18, some positions from chr3 in hg19 are matched to chr2 in hg18. e.g. chr2:5144329 in hg19 are matched to chr3:165545129
Does anyone know why?
Does anyone know why?
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Interesting; I have not seen that. It looks like portions of the chromosomes were rearranged between the different assemblies. If you download the liftOver hg19 to hg18 chain file and type inyou will see:Code:grep 'chr 2' [hg19_to_hg18_chainfile] | grep 'chr 3' | less
The position you listed would fall within the last line.Code:chain 25982 chr2 243199373 + 16340754 16341023 chr3 199501827 - 118072788 118073057 6523537 chain 4737 chr2 243199373 + 5145834 5145884 chr3 199501827 - 155139362 155139412 33407240 chain 4607 chr2 243199373 + 5145066 5145350 chr3 199501827 + 191348934 191349218 1967131 chain 2538 chr2 243199373 + 16338477 16338504 chr3 199501827 - 154040818 154040845 35425972 chain 1237 chr2 243199373 + 5143151 5144336 chr3 199501827 - 33955506 33956705 3724972
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have you tried to look at the sequence to see if its the same?Comment
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Cancer survival rates have significantly increased in the last few decades in the United States, reaching a combined 70% 5-year survival rate by 2021. Behind this number, there are years of research to find new therapies, drug targets, and early detection methods. But there is one core challenge that keeps slowing down these advances, and it’s about drug resistance.
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Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.07-01-2026, 11:43 AM
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...
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