RNA-seq READS mapping on Reference Genome

[kumardeep]

Hi all
I am new entrant on this platform. I am a tyro on NGS analysis. What motivated me to come into this field is basically emergence of NGS data exponentially. Also presently my project is analyzing the RNA-seq data.
I want to align RNA-seq data (READS) of a experiment related to prostate cancer in human on the reference genome. I don't know which reference genome should I take for mapping upon. Is it right to take hg19 whole human genome from UCSC genome browser site ? OR should I take genome specific for prostate cancer only ?

Thanks in advance.
Kumardeep

[kopi-o]

hg19 is fine.

[kumardeep]

Thanks for the suggestions.

[kumardeep]

Hi
I downloaded the hg19.2bit file from UCSC browser site. Then converted that into fasta format using twoBitToFa utility. hg19.2bit was ~778 MB and hg19.fa was 3 GB. But when I opened that .fa file it contained some extra chromosomes (e.g. chr21_gl000210_random, chrUn_gl000245,chr6_mcf_hap5) besides conventional autosomes and X and Y chromosomes; and the total chr count went to 93. I don't know whether to use this whole file for mapping RNA-seq reads or only those chromosomes which are conventional (autosomes and X/Y). Furthermore, what is the meaning of these variant chromosomes as mentioned above.

[kopi-o]

I think most people just use the "conventional" ones. The others are describing, e.g., different haplotypes of hypervariable regions. They are mostly interesting for specialized analysis.

[ETHANol]

Welcome to the world of NGS. Map your reads to hg19 with Bowtie (or some other aligner if you like).

You can play around with the setting some and see what different options do.

When you are comfortable with that give Tophat a try. It is painfully slow but will map across splice junctions. You will need a GTF file for that, which you can find along with a bunch of other stuff here:
ftp://igenome:[email protected]_hg19.tar.gz

http://tophat.cbcb.umd.edu/igenomes.html

You may also be interested in some of the stuff I have written on my blog at:

http://ethanomics.wordpress.com/

Good luck.

[kumardeep]

Thanks for the guidance. Sure, will go through these links and see what I get ..........