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Old 08-17-2017, 09:06 AM   #1
Jane M
Senior Member
Location: Paris

Join Date: Aug 2011
Posts: 239
Question Extracting alternate loci from fasta genome

Dear all,

I downloaded full reference fasta genomes for hg19, mm9 and mm10 from gencode. They include reference chromosomes, scaffolds, assembly patches and haplotypes.
For a specific purpose, I want to remove haplotypes.
I did not manage to find a description of the nomenclature used for the contigs in fasta file.
In the hg19 reference genome I use, there are 297 contigs. One can see for example:
>chr1 1
>chr2 2
>chrM MT
>GL877870.2 HG1007_PATCH
>GL877872.1 HG1032_PATCH
>GL383545.1 HSCHR10_1_CTG2 <- is it an "unlocalized sequence" ?
>GL383546.1 HSCHR10_1_CTG5
>GL000191.1 GL000191.1
>hg19GL000192.1 GL000192.1
I would like to know how many of them are haplotypes and which ones are they.
Is there a way to get this information?

Thank you in advance for your help.
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Old 08-18-2017, 09:37 AM   #2
Jane M
Senior Member
Location: Paris

Join Date: Aug 2011
Posts: 239

If it can help someone in the future, we can get this type of information on NCBI:
In *_report.txt files, for each contigs, there is assembled-molecule / unlocalized-scaffold / unplaced-scaffold / novel-patch / fix-patch or alt-scaffold.
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