About Mouse Reference Genome

Question

[Tonyzeng]

I have a question here, when I download mouse reference genome, this package has chr.fa, *Un.fa, Hap.fa and random.fa in it. before I concatenate them together for BWA alignment, Do I have to remove these .fa files which have Un, Hap, Random or it is unnecessary?

Answer 1

[Ashutosh Pandey]

You should keep all the chromosomes, Un and Random. Never heard of Hap though, you should probably remove the Hap. Can you give me the link from where you downloaded all these files. I may check and tell you if Hap is important or not. I dont think it is important for now.

[Tonyzeng]

Thank you, ashuoshmits. I am sorry that Hap.fa is just in human reference genome but not in mouse. I downloaded it from http://hgdownload.cse.ucsc.edu/goldenPath/mm10/bigZips/

I deleted Un and Random just because I found some groups deleted Un and random of mouse genome before they do alignment, so should I still keep all the chromosomes?

[Ashutosh Pandey]

I think you should keep them in order to reduce number of false SNPs.

Answer 2

[Ian]

The 'hap' contigs are different haplotypes constructed on different chromosomes. I remove them because they will will result in duplicated sequence and effect your mapping. When I perform ChIP-seq analysis I then remove any reads mapping to unassembled contigs and the mitochondrial genome. Especially chrM as it effects the FDR calculation in MACS.