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human genome

human genome - Bioinformatics

human genome - Have questions about bioinformatic tools or databases? Post questions here. Discuss and post interesting bioinformatics information.


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  #1  
Old 06-12-2010, 06:05 AM
Pipette Filler
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Default human genome



seems that currently 9 human genomes are publically available (or 12 ?)
list here:

some can be downloaded in large (~200MB, some are compressed with gzip) files
in format ".gff" with ~2M lines, one line representing one nucleotide-change
(to what ?) with chromosome name and position and changed nucleotide.

but the format of the files is different, has someone a computer-readable list
of all genome-mutations ?
Where can we share such lists ? Discuss the data-generation and analysis ?

So far I converted JW


I found this thread:



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  #2  
Old 06-12-2010, 11:21 AM
Pipette Filler
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Default Re: human genome

it seems easy as i understand but tell more about your purpose.
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  #3  
Old 06-13-2010, 05:47 AM
Pipette Filler
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Default Re: human genome

it's tedious, though, with these long files.
So I think these files should be converted and offered in uniform
standardized computer-readable format somewhere.

Is anyone else here working with these files ?

-------------
first 3 lines in my file jw.d (differences in James Watson's genome to some (which ?) standard)
01, 41921,GC,BJW-1117373
01, 42101,TG,rs2691277.1
01, 45408,CT,rs28396308
...
chromosome,position,old+new nucleotide,gene-name(?)

~2M lines, 54MB uncompressed, maybe genename isn't needed

now make the same format for YH,...


--------------------------

Code:
file JW.gff ,  filed,name,counts
1.) chr1,163479  chr2,174209  chr3,142245  chr4,148282  chr5,126170
    chr6,129906  chr7,111889  chr8,106542  chr9,86346   chr10,105298
    chr11,105511 chr12,96403  chr13,83250  chr14,64540  chr15,61959
    chr16,62665  chr17,53075  chr18,59829  chr19,38679  chr20,43857
    chr21,31727  chr22,24906  chrX,38031   chrY,1746
2.) JW,2060544
3.) genotype,1840461 
     gt_novel,220083
4.) 2049126 numbers   , chr1:<247M
5.) same 2049126 numbers 
    maximal values :
    chr01:247175763 chr02:242691366 chr03:199365024 chr04:191262790 
    chr05:180643418 chr06:170762121 chr07:158818812 chr08:146266634 
    chr09:140218908 chr10:135374311 chr11:134451246 chr12:132288869 
    chr13:114118283 chr14:106360250 chr15:100338311 chr16: 88690776 
    chr17: 78643154 chr18: 76116029 chr19: 63789120 chr20: 62433614 
    chr21: 46944097 chr22: 49570097 chr X:154874055 chr Y: 57442498
    sum:3077M
6.) .,2060544
7.) +,2060544
8.) .,2060544
9a)  SNP rs: 1840461   SNP BJW: 220083    2060544 numbers in total
9b)  alleles A/C;,86738
     alleles A/G;,342479
     alleles A/T;,73416
     alleles C/A;,91673
     alleles C/G;,86143
     alleles C/T;,348865
     alleles G/A;,349743
     alleles G/C;,86305
     alleles G/T;,92397
     alleles T/A;,73611
     alleles T/C;,342446
     alleles T/G;,86728
9c) ref_counts 0,382024
    ref_counts 1,387528
...
9d) oth_counts 1,602522
...

Last edited by gsgs; 06-13-2010 at 06:20 AM.
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  #4  
Old 06-14-2010, 10:05 AM
Pipette Filler
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Default Re: human genome

Code:
02  |  asw  ceu  chb  chd  gih  jpt  lwk  mex  mkk  tsi  yri  
----+--------------------------------------------------------
asw |    0  128  164  163  136  174  166  123  145  128  100 
ceu |  128    0  172  129   84  152  212   95  169   84  150 
chb |  164  172    0  121  140  116  208  161  207  136  194 
chd |  163  129  121    0  115   77  231  150  182  121  163 
gih |  136   84  140  115    0  124  222  111  169   78  168 
jpt |  174  152  116   77  124    0  214  149  201  124  172 
lwk |  166  212  208  231  222  214    0  193  175  202  140 
mex |  123   95  161  150  111  149  193    0  192  113  149 
mkk |  145  169  207  182  169  201  175  192    0  157  129 
tsi |  128   84  136  121   78  124  202  113  157    0  156 
yri |  100  150  194  163  168  172  140  149  129  156    0
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