GWIPS-viz Forums

Full Version: hg19 vs hg38
You're currently viewing a stripped down version of our content. View the full version with proper formatting.
Why are there two different sets of studies for hg19 and hg38?
Since the data are being processed starting from reads, presumably, one should be able to map data from all of the studies to both hg19 and hg38 assemblies. I wonder what the reasons were to choose one assembly over the other for each of the studies.
Hi there,

The reason is because when we started GWIPS-viz, the hg19 assembly only was available and so the older data sets are mapped to this assembly. When the more recent hg38 assembly became available we had wanted to do a lift-over for these older data sets, but it was not very satisfactory. Hence, the reason why older data sets are available for hg19 only and more recent data sets available for hg38.

Thanks for your interest,
Audrey
Thank you Audrey. Are there any plans to map the old datasets to the latest assembly? Given the relatively small number of studies for initiation sites, I feel any additional data can be very helpful.
Hi,

Yes, we plan to re-map the older data sets to hg38. We will start with the studies with enrichment for initiation sites. Unfortunately I can't really say how soon these will be available but I will post when they are done.

Thanks again,
Audrey
By 're-map' I presume you mean re-processing the data using hg38 and not remapping the hg19 data to hg38...

You have mentioned that the liftover results were unsatisfactory. Would you mind elaborating a bit on that? NCBI also provides coordinate remapping service (https://www.ncbi.nlm.nih.gov/genome/tools/remap). I wonder if the results using these alignments would be more acceptable.
Reference URL's