I'm looking to run cufflinks on an RNA-seq data set to annotate and assemble sequence reads. I normally use GENCODE v19 for this but the lncRNA RNA gene I am interested in is not annotated in the GTF file. The gene is 'LOC100506023' which has the RefSeq accession 'NR_037845.1'. It does not have a GENCODE or Ensembl accession. Does anyone know if a RefSeq GTF file exists for the latest genome build and where I can download it from? If not RefSeq, then another annotation file that contains the RNA gene above. Thanks.
Use the table browser at the UCSC Genome Browser to make and download a RefSeq GTF file to use.
http://genome.ucsc.edu/cgi-bin/hgTables
Use the table browser at the UCSC Genome Browser to make and download a RefSeq GTF file to use.
http://genome.ucsc.edu/cgi-bin/hgTables
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