Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer version?
2
0
Entering edit mode
5 weeks ago
Ali • 0

We are using previously published RNA-seq data for a new project, which was mapped in 2018 to an older GRCh38 version. Is it worth re-mapping to GRCh38.p14 so we have the most up-to-date build at the onset?

RNA-seq patch freeze genome • 436 views
ADD COMMENT
0
Entering edit mode

If you have a one-click workflow ready and the necessary computation power to casually run it, then go for it. If it is any greater effort or costs money then no. It is just a minor update within an existing genome. Still, if data are published and you uploaded e.g. raw counts at GEO then you could simply use that. Somewhat helps with reproducibility as you can just pull an existing file and go. Also easy to publish your code based on publically-available files without the need to do any more processing.

ADD REPLY
0
Entering edit mode

most up-to-date build

Major build of the genome remains GRCh38. What you are looking at is the latest patch release for that build. Only changes are likely to be in annotations as noted below.

ADD REPLY
2
Entering edit mode
5 weeks ago
DGTool ▴ 40

At least so far to my knowledge, I don't think it would be worth re-mapping to GRCh38.p14, if it is too much trouble or with what you're looking at is unaffected by the updates in the minor releases. The minor releases of the assembly (i.e. indicate by the *.p14) are patches to certain parts of the assembly without changing the actual chromosome coordinates (so assuming it would be more related to small changes in annotation). There is some more information about what these patches contain here: NCBI Patches; and a slightly different but somewhat similar question here

ADD COMMENT
1
Entering edit mode
5 weeks ago

We get this question like clockwork every 6 weeks.

I'll say it one more time:

A freeze is a freeze.

Patches are not a thing that 99% of people will need to worry about or can even use in any meaningful manner.

https://www.biostars.org/post/search/?query=patches

ADD COMMENT

Login before adding your answer.

Traffic: 1299 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6