I have a file including different accession numbers from RefSeq Protein of chicken genome and I want to convert them into the "Gene symbols". I tried to use bioDBnet - db2db to get the conversion. However when I want to donwload the full results (~50000) I only get in the downloaded file a part of the results (< 12000)
Is there an other way to run bioDBnet or an other tools to get the same results? (R packages, scripts)?
It tried also with BioMart but strangely I get 0 results. I selected chicken genes, then in filter Input external references ID list - RefsSeq pepitdes ID for my NP number. I tried also gProfiler but for many refsSeq I have none gene symbol
a part of my accession numbers are like below: NP_001001127.1 NP_999839.1 XP_001231206.2 XP_430508.3 YP_009555261.1
Thanks for the sugestions
I suspect if you remove the trailing
.1from the RefSeq IDs you'll get some results from Ensembl BioMart.
Yes you are right, removing .1 make it work. But still have missing results using biomart unfortunatly.
If you're trying to map exclusively between NCBI identifiers, it's probably best to avoid Ensembl. An Ensembl ID will always be the reference in their datasets, so you end up doing more conversions behind the scenes with more potential for non-one-to-one mappings.