ensembl-gene-info file hg19

[patidarr]

Hi,

Could you please share the hg19 version of this file for rnaseq cnv analysis or show me what columns it should have if my rsem output looks like following:

` gene_id transcript_id.s. length effective_length expected_count TPM FPKM 6M1-18 uc010jrh.1 473 272.4 0 0 0 7M1-2 uc003wdr.3 68 0 0 0 0

`

[etal]

Unfortunately I didn't see hg19 available in Ensembl BioMart, where the hg38 files came from.

The columns I retrieved from Ensembl BioMart were:

• "Gene stable ID" -- Ensembl ID
• "Gene % GC content"
• "Chromosome/scaffold name"
• "Gene start (bp)"
• "Gene end (bp)"
• "Gene name"
• "NCBI gene ID"
• "Transcript length (including UTRs and CDS)"
• "Transcript support level (TSL)"

The first column in this gene resources file, called gene_id internally, needs to match the gene_id column of your RSEM file. So if you ran RSEM with Ensembl's transcript annotation, these should be Ensembl gene identifiers. Otherwise, if you used another transcript annotation, you'll need a BioMart instance with that annotation's gene identifiers.