ENSEMBL Transcript_Accession ID conversion

Question

[dinindu.senanayake]

Hello, I have used Kallisto by PachterLab take a look at my Mouse: RNASeq data at a Transcript level by using the Pseudoalignment method. However, the abundance files generated at the end of the analysis converted the transcript_accessions_ID to it's isoform format as below

ENSMUST00000142260.2
ENSMUSG00000021252.6
ENSMUST00000021676.6
ENSMUST00000124311.1
ENSMUST00000148323.1
ENSMUSG00000007777.4

What would be the best way to convert these into MGI:Gene ID or ENSEMBL gene ID?

[ta_awwad]

@dinindu.senanayake have you successfully solved this problem?

[WouterDeCoster]

Please use ADD COMMENT or ADD REPLY to answer to previous reactions, as such this thread remains logically structured and easy to follow. I have now moved your post but as you can see it's not optimal. Adding an answer should only be used for providing a solution to the question asked.

Answer 1

[mastal511]

You already have Ensembl gene IDs. ENSMUSG00000021252.6 and ENSMUSG00000007777.4 are Ensembl gene IDs.

Answer 2

[WouterDeCoster]

Cut of the .2 etc notation, and download a dataset from http://www.ensembl.org/biomart/martview/99531bd013196fddd72a5dfe04d48c32. You can for example use dplyr to perform a left_join on your table and the table derived from biomart. Need more pointers?

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edit: as pointed out by someone more awake than myself, you already have ensemble gene identifiers. Not what you had in mind?