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,
•
written
by
Fawzi Yassine •
1 answer
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'.
Log in to answer this question.
-
Purpose and necessity of removing PCR duplicates in m6A-seq analysis
written by remagen •
-
Aligner logic
written by Lenny186 •
-
Low assigned alignments
written by Simon Ahn •
-
Newbie questions about Methyl-Seq (Bismark)
written by wester1086 •
-
Reference Transcriptome for hg19
written by stefanos.bamopoulos •
-
How can a gene exist on three different chromosomes!?!?
written by sviatoslav.kendall
-
A couple of questions related to transcriptome assembly (Using Cufflinks/Scripture)
written by daniel.soronellas
-
News: The New Grch38 Human Genome Browser Has Arrived!
written by Giovanni M Dall'Olio
-
Problem Using Gencode Gene Annotation Gtf With Tophat And Discrepancy Between Ucsc/Gencode Gtfs
written by Ian
-
Is It Normal For Cufflinks Produce Different Results In Multiple Runs
written by Superligang •
