Hi,
I have about 3000 miRNA targets from miRDB. I am needing to convert the target identifiers into Ensembl ids (mouse btw). About 2k of these convert using biomaRt in R. The other 1k I am not sure how to handle programmatically as I can't figure out what id type they are.
Most convert using either refseq_mrna (Refseq mRNA ID(s) [e.g. NM_001195244]) or refseq_mrna_predicted (Refseq Predicted mRNA ID(s) [e.g. XM_889253])
An example of one that doesn't convert: "NM_001042565". Looking this up in Ensembl via the main search I get "novel transcript (Mouse Transcript)". So I know it is there. I have taken the identifier and tried to convert it using Ensembl's BioMart using the filter option with most of the gene/transcript looking options and do not get anything back.
What filter option should I use to get all the miRDB target id's to convert to Ensembl IDs???
Thanks,
Bob
I have about 3000 miRNA targets from miRDB. I am needing to convert the target identifiers into Ensembl ids (mouse btw). About 2k of these convert using biomaRt in R. The other 1k I am not sure how to handle programmatically as I can't figure out what id type they are.
Most convert using either refseq_mrna (Refseq mRNA ID(s) [e.g. NM_001195244]) or refseq_mrna_predicted (Refseq Predicted mRNA ID(s) [e.g. XM_889253])
An example of one that doesn't convert: "NM_001042565". Looking this up in Ensembl via the main search I get "novel transcript (Mouse Transcript)". So I know it is there. I have taken the identifier and tried to convert it using Ensembl's BioMart using the filter option with most of the gene/transcript looking options and do not get anything back.
What filter option should I use to get all the miRDB target id's to convert to Ensembl IDs???
Thanks,
Bob
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