find a correct gene symbol for lncRNA

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4.8 years ago

naghmeh_saedi • 0

I have a lncRNA list with transcript id. How I can find the correct gene name for each transcript Id?

RNA-Seq • 1.1k views

ADD COMMENT • link 4.8 years ago by naghmeh_saedi • 0

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naghmeh_saedi : Always provide examples when you are asking about ID's?

ADD REPLY • link 4.8 years ago by GenoMax 147k

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No my list is about these IDs XLOC_000023, XLOC_000208, XLOC_000948, XLOC_000356. and I need gene symbol in order to analyse my subject. I need a package or software to convert these ID to gene symbol.

ADD REPLY • link 4.8 years ago by naghmeh_saedi • 0

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See this past thread: How to get Ensembl ids in cuffdiff output?

What kind of annotation file (if any) did you use originally?

ADD REPLY • link 4.8 years ago by GenoMax 147k

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Is this an Ensembl transcript ID? If so, you can use Ensembl BioMart to obtain tables that relate transcript and gene IDs.

ADD REPLY • link 4.8 years ago by mark.ziemann ★ 1.9k

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No, these transcript Id is related to LncRNA.

ADD REPLY • link 4.8 years ago by naghmeh_saedi • 0

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