About hg19 reference genome

Question

[luckysardar171]

Hello biostars

I am trying to get some information from paper its genecount with genename. according to my research of interest I need chromosome information and gene id for that i have downloaded ensemble GRCh37, genecode ref and biomart also tried match genename not able get info of all the genes can anyone help why am missing lot of genes. In paper mentioned they used hg19 ref genome out of 36000(combining two replicates) genes i am getting 28000 genes info in biomart roughly can anyone suggest me how to get the correct GTF file for hg19 ref genome

Thank you

Answer 1

[hakimbazol]

I think the GTF file from UCSC genome browser will be enough. Just to be careful that sequences are divided into exon, 3-UTR and 5-UTR, that may little confusing when you look at the first time.

You can download it here https*://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/

[luckysardar171]

hakimbazol i have tried this still not all genes are matching with the genecounts file given