Mapping using UCSC and counting using RefSeq

Question

[Fawzi Yassine]

Hi, I am analyzing public RNA-seq data to find genes differentially expressed between diseased patients and controls. The paper for which the paper belong says: ” The reads were mapped to human genome (hg19) by TopHat. The number of fragments in each known gene from RefSeq database (downloaded from UCSC Genome Browser) was enumerated….”

Q1: Are the 2 files compatible? (one file used for Mapping using UCSC hg19 Genome but another file used for annotation was downloaded from TableBrowser using track Refseq ) Q2: which track shall I use? ‘NCBI Refseq’ or ‘Other Refseq'. Thank you,

Answer 1

[David Langenberger]

The two files are compatible, if for the gene annotation file the 'hg19' assembly (same as genome assembly) was selected. The genome file holds the sequence of the human genome and the gene annotation file holds the predicted genes from the RefSeq database for this genome. First file is a fasta file and the second file probably a bed file with genomic locations of genes. Use the NCBI RefSeq file and not the 'Others RefSeq'.