Its possible to merge GTF files from different genome versions so I can assing the seqnames from one ot another
0
0
Entering edit mode
3 months ago
Nicolas • 0

Hello everybody I have two GTF files of two different version of a genome and I like to merge both so I can have the equivalence of the seq names as in the oldest version they were named in the way HSymV2.0_g01.00001_t1 and in the newest they are named in the way NC_079875.1, and I need the gene functional and domain annotations but they are avaiable with the first naming type. is it possible to do?

Genome GTF • 513 views
ADD COMMENT
0
Entering edit mode

Please define how you plan on "merging" these files. It looks like you need more of a rename/name-mapping operation than a merge operation.

ADD REPLY
0
Entering edit mode

Hello I mean if I can assign the old gtf gene ids in the form of HSymV2.0_g01.00001_t1 to the new version gtf file by the genomic coordinates so I can extract GO KEGG PFAM and InterProScan data from the original article of the assembly, I don't know if what I want to do its its rename or re mapping or if it is possible to do

ADD REPLY
0
Entering edit mode

See answers here: Are there any alternatives to Liftoff - Mapping annotations (GFF/GTF) between assemblies

Line serves to satisfy biostar spam check.

ADD REPLY

Login before adding your answer.

Traffic: 1469 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