I have a set of data which has RefSeq Id of a transcript. I am unable to get unique Ensembl transcript Id for the refseq.
I've tried Biomart as suggested by some previous post but first of all they didn't give unique mappings to Ensembl and approx 6K of the refseq id cannot be find in the table.
Also tried UCSC mysql thing, the way they have suggested is, using table mrnaRefseq but when I try to get the table using command
mysql --user=genome -N --host=genome-mysql.cse.ucsc.edu -A -D hg19 -e "select * from mrnaRefSeq" > test1.txt
I get
ERROR 1146 (42S02) at line 1: Table 'hg19.mrnaRefSeq' doesn't exist
Any suggestion guys?
Data can be found here. Second column of the data is relevant Refseq Ids
This should work with the UCSC table browser:
https://genome.ucsc.edu/cgi-bin/hgTables
Select assembly: hg19, track: Ensembl Genes, output format: selected fields from primary and related tables and then "get output". Under linked tables pick hg19.knownToEnsembl, hg19.knownToRefSeq and hg19.kgXref (using allow selection button at the bottom in-between). Then just check whatever columns you want (gene symbol, ensembl ID, RefSeq ID, etc.) and press "get output". This should create a tab-delimited file with the desired information.