Timeline for How good does the assembly of an NCBI prokaryotic genome have to be in order to argue gene loss?
Current License: CC BY-SA 4.0
4 events
| when toggle format | what | by | license | comment | |
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| Jul 1, 2022 at 20:07 | vote | accept | Laura | ||
| Jul 1, 2022 at 17:52 | comment | added | Maximilian Press | @Laura yes, I believe that's accurate. Many things are lost/misassembled during assembly that are obviously present in inspecting raw data. You would be looking for a similar coverage to the rest of the genome, unless you expect some funny business in that regard. The issues that arise are in the case of repetitive or highly homologous sequences, which is more of an issue in metagenomics as you might have separately binned closely related or homologous genomes. For example if you have abundant genome A, that will tend to suck up a lot of reads for homologous sequences in genome B. | |
| Jul 1, 2022 at 7:46 | comment | added | Laura | Thank you! Regarding your last paragraph, are you saying that it is probable that genes would be lost during assembly / binning (therefore not fully trusting a non-complete assembly), but not so much during sequencing (therefore trusting the raw data)? I imagine that might not hold for low sequencing depths, though. I was wondering, how high do you thing the sequencing depth have to be in order for the raw data to be reliable in terms of gene absence? | |
| Jun 30, 2022 at 19:40 | history | answered | Maximilian Press | CC BY-SA 4.0 |