ordered genome ?

Question

[Siva]

Hi friends,

Got a small doubt about a genome file. I don't know if my chromosomes are already ordered in my fasta file

Actually I think it is because it's not 1 to 17.

Just want to confirm with you before to extract the region I wanted after a blast. My indexed genome order:

	chr0 359367108 24 60 61
	chr1 175985764 365356603 60 61
	chr10 327788049 544275484 60 61
	chr11 208730832 877526688 60 61
	chr12 208068730 1089736388 60 61
	chr13 239367298 1301272951 60 61
	chr14 230295834 1544629724 60 61
	chr15 202246870 1778763842 60 61
	chr16 226777971 1984381514 60 61
	chr17 267415242 2214939138 60 61
	chr2 209013747 2486811320 60 61
	chr3 203472901 2699308649 60 61
	chr4 216026857 2906172785 60 61
	chr5 271056985 3125800109 60 61
	chr6 100519666 3401374730 60 61
	chr7 109221022 3503569743 60 61
	chr8 192129815 3614611135 60 61
	chr9 253478808 3809943133 60 61
	cp_gi_8 151104 4067646615 60 61
	mt_gi_5 300945 4067800266 60 61
	rDNA_gi_5 9814 4068106255 60 61

view raw gistfile1.txt hosted with ❤ by GitHub

Advance thanks

[iraun]

I would like to help you but I don't really understand your question.
Do you want to sort the chromosomes in your fasta file? The file you have attached it is sorted alphabetically, not by chromosome. What are you trying to do exactly?

[Siva]

I search a way to know if chromosomes of my genome are in this order.
Actually I got a genome file, and wanted to locate some genes and retrieve the part of the genome, but before that I should know if my genome has already ordered chromosomes.

[iraun]

I would suggest you to do that using bedtools getfasta. Read here for more info: http://bedtools.readthedocs.org/en/latest/content/tools/getfasta.html.

[Siva]

Nope airan I can't make a bedtools because haven't got bed file, and i don't want to retrieve sequences.
The file I give before is already from samtools faidx so no use to take that to make a getfasta.
I just want to know if the genome I have is already a contiguous one so with a good order of his chromosomes.

[Raony Guimarães]

Your .fasta file doesn't seen to be "karyotypically" ordered.

You should read this question -> Karyotypically Ordered Hg19

A simple way to check the order in your fasta file would be:

grep ">" filename.fasta

[Siva]

Yeah when I did a grep I got the same order than in this file:

	chr0 359367108 24 60 61
	chr1 175985764 365356603 60 61
	chr10 327788049 544275484 60 61
	chr11 208730832 877526688 60 61
	chr12 208068730 1089736388 60 61
	chr13 239367298 1301272951 60 61
	chr14 230295834 1544629724 60 61
	chr15 202246870 1778763842 60 61
	chr16 226777971 1984381514 60 61
	chr17 267415242 2214939138 60 61
	chr2 209013747 2486811320 60 61
	chr3 203472901 2699308649 60 61
	chr4 216026857 2906172785 60 61
	chr5 271056985 3125800109 60 61
	chr6 100519666 3401374730 60 61
	chr7 109221022 3503569743 60 61
	chr8 192129815 3614611135 60 61
	chr9 253478808 3809943133 60 61
	cp_gi_8 151104 4067646615 60 61
	mt_gi_5 300945 4067800266 60 61
	rDNA_gi_5 9814 4068106255 60 61

view raw gistfile1.txt hosted with ❤ by GitHub

The question is: so in my genome the order of the chromosomes is what it's given by the grep result?

It could not be an other order ? In the real genome we'll find it in that order, am I right?

[Ashutosh Pandey]

grep will give you the same order as chromosomes appear in your fasta file. If you want to change the order of chromosomes and create a new file, you should be able to do it using Picard. Search biostars for relevant posts. You can use keywords such as "change order chromosomes fasta".

[Siva]

OK thanks guys.

I think chromosomes are conserved in the genome, I'll continue with that.

P.S.: I don't want to change the order, just wanted to confirm the real order in the real genome.

Answer 1

[Alex Reynolds]

Ordering is whatever you need it to be. Some common sorting schemes (sort-bed, for instance) use "lexicographic" ordering of chromosome names, so as to take advantage of that structure. In that scheme, the chromosome label "chr11" is positioned before "chr2", for example. Other schemes can use numeric sorting, where "chr2" would come before "chr11". It just depends on where your data come from and what you need to do.