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updated 22 months ago by
Ram
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written 9.5 years ago by
Siva
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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?
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.
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.
Yeah when I did a grep I got the same order than in this file:
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?
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updated 22 months ago by
Ram
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written 9.5 years ago by
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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".
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.
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?
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.
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.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.
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:
Yeah when I did a grep I got the same order than in this file:
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?
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".
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.