4 ms·

While using the software packages released last week may not be the greatest idea, I am leery of any research paper using 10 years old genome assembly, Ensembl

While using the software packages released last week may not be the greatest idea, I am leery of any research paper using 10 years old genome assembly, Ensembl annotation release in the 40ish (we are at #105 ) or clearly outdated program versions with X updates in the last 5 years. Also if Fedex/UPS were tracking packages with bordering on cavalier attitude observed in some labs, often we would be getting bags of guano ordered by some horticulturalist instead of a book of our choice. Or even an empty bag, since QC may be an afterthought and hard wet lab work may still produce unusable crappy data. On the other hand the brand new technologies are rather expensive, good quality human tissue samples hard to get so scrapping the bottom of the barrel trying to justify grant $$$ is unavoidable.

stonemetal12 4y ago
>Ensembl annotation release in the 40ish (we are at #105 ) Were there any major bug fixes that would impact their work in that time window? Maybe for them it is done instead of outdated.
- elmolino89 4y ago
  Sure. Some genes were retired because there was not enough support. Earlier Ensembl versions used older genome assembly. Which means: some genes "jumped" from one chromosome to another, or got properly stitched residing before partially on floating contigs. Just to be clear: I am not saying that anything done in 2022 using hg19 is 100% wrong. Just that it is a bit like using a stretched shoelace 50cm (+/- 5cm) to measure your corridor when you have a decent tape measure in your pocket. There are microarrays used in Big Science projects with ~1/3 of probes not matching human transcripts from latest ENSEMBL. Since most of them map to the current genome who knows what is the meaning of the signal from such probes. Unannotated exons? Retained introns? But some probes do not even map to the genome => some silly splicing error(?) packed in a plasmid in the 90ies?

stonemetal12 4y ago

>Ensembl annotation release in the 40ish (we are at #105 ) Were there any major bug fixes that would impact their work in that time window? Maybe for them it is done instead of outdated.

elmolino89 4y ago
Sure. Some genes were retired because there was not enough support. Earlier Ensembl versions used older genome assembly. Which means: some genes "jumped" from one chromosome to another, or got properly stitched residing before partially on floating contigs. Just to be clear: I am not saying that anything done in 2022 using hg19 is 100% wrong. Just that it is a bit like using a stretched shoelace 50cm (+/- 5cm) to measure your corridor when you have a decent tape measure in your pocket. There are microarrays used in Big Science projects with ~1/3 of probes not matching human transcripts from latest ENSEMBL. Since most of them map to the current genome who knows what is the meaning of the signal from such probes. Unannotated exons? Retained introns? But some probes do not even map to the genome => some silly splicing error(?) packed in a plasmid in the 90ies?