Should I use chrM,random and haploid fasta file to build hg19?

[mozart]

Dear all,
I have downloaded the hg19 from UCSC and want to combine all the chromosome together to generate the reference genome to be indexd in BWA. However, there are some files like chrUn_g*.fa, chr1_gl*_random.fa, and chrM.fa. Should I combine these files together with the autosome and X,Y
chromosome or throw them away before build the reference genome?

Thanks a billion!

June

[Richard Finney]

Use chr1-22,X,Y,M
...or ...
Use them all except the hap ones!!!
Either way is fine.

Many people stick with 1-22,X,Y,M to keep things simple.


The "hap" ones are alternate assemblies for certain regions.
DO NOT USE THE *hap* files !!!!

[lh3]

Use this:

ftp://ftp.ncbi.nih.gov/1000genomes/f...k_v37.fasta.gz

If you prefer to build your own, include those _random.

[Kaonashi]

Hi! I hardly recommended to use chrUn_g*.fa, chr1_gl*_random.fa, and chrM.fa for reducing miss alignment reads from these scaffolds.

[mozart]

Thanks a billion for the kindness and help from all of you. By the way, what are the exact meanings of the file chrUn_g*.fa, chr1_gl*_random.fa ?

[ishmael]

Thanks a billion for the kindness and help from all of you. By the way, what are the exact meanings of the file chrUn_g*.fa, chr1_gl*_random.fa ?

For what I know, these are the contigs of genome that are not quite sure the exact position. Because there are many factors effect the assembling of genome, so some contigs the consortium didn't integarate with whole genome, just labeled as chrUn_* (not sure which chromosome come from) or chr1_*_random (from chr1 already known). And for hg19, there are patches released when the consortium integerate the contig with genome (in hg19, the coordinates are reversed for contigs, so in the version hg19, the integeration doesn't effect the already sequence coordinates).
More information you may check this:

http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/info/definitions.shtml

For what I checked, some chrUn contigs have also some variants of rRNAs or such things. But I think it is not a serious thing.

[mozart]

So grateful for your reply. Because I only need the count data but not the variants, the deletion of that random contigs might be better to avoid confusion.

[dejavu2010]

more questions

what is hap region? thx