How To Get Sequences Of Rna-Seq Transcripts Isoforms From Tcga ?

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10.8 years ago

jack ▴ 520

Give you have UCSC IDs of transcript isoforms of genes from TCGA. The goal is to find the sequences of this isoforms. Does anybody know webserver/software which fit into this scenario?

example of IDs:

uc001jiu.2   
uc002bgz.2        
uc002bic.2        
uc010qhg.1    
uc010unu.1       
uc010uoa.1        
uc010zzl.1   
uc011krn.1       
uc011lsn.1

genomic ucsc transcript rna-seq tcga • 3.2k views

ADD COMMENT • link updated 10.8 years ago by Neilfws 49k • written 10.8 years ago by jack ▴ 520

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This is quite easy to do using either the UCSC website or BioMart. However: as I commented on your previous question - How to map isoform IDs of transcript to Entrez IDs ? - none of those IDs are valid, when pasted into the UCSC Table Browser. You should figure out why before continuing.

ADD REPLY • link 10.8 years ago by Neilfws 49k

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