Get SYMBOL using mapIds with T2T genome ?
0
0
Entering edit mode
4 months ago
Picasa ▴ 650

Hi I use to retrieve symbol from ENSEMBL id using this function:

 resOrdered$symbol <- mapIds(org.Hs.eg.db,
                     keys=row.names(resOrdered),
                     column="SYMBOL",
                     keytype="ENSEMBL",
                     multiVals="first")

but it only works with the hg38 genome. Is there an alternative with the T2T genome and annotation ?

t2t • 295 views
ADD COMMENT
0
Entering edit mode

Is there an alternative with the T2T genome and annotation ?

T2T assembly is available via Ensembl rapid release, if you need Ensembl ID: https://rapid.ensembl.org/Homo_sapiens_GCA_009914755.4/Info/Index

ADD REPLY
0
Entering edit mode

So the only way is to write a script that extract the symbol from the gtf file ?

ADD REPLY

Login before adding your answer.

Traffic: 2045 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