Thanks, Tej.
I tried as you suggested, in the knownGene part, I pasted the gene names:
PIK3CD
MPL
But doing as you suggested, there is no output, only showed
#hg19.knownGene.chrom hg19.knownGene.txStart hg19.knownGene.txEnd hg19.kgXref.kgID hg19.kgXref.geneSymbol
I then check the description for Paste in identifiers for UCSC Genes, it showed below,
Please paste in the identifiers you want to include. The items must be values of the name field of the currently selected table, knownGene, or the alias field of the alias table kgAlias. (The "describe table schema" button shows more information about the table fields.) Some example values:
uc001yuc.1
uc002fpj.1
uc010nxl.1
NP_055440
NP_001611
Q9H7G3
Looks like I couldn't directly paste the gene names here?
Any comments?
Cant you get that from GTF file?
Gencode GTF
A: Converting gtf format to bed format
Ensembl GTF