[BioC] BSgenome

[James W. MacDonald]

This may help clear things up for you:

http://genome.ucsc.edu/FAQ/FAQdownloads.html#download9

Best,

Jim



On 7/14/2014 5:03 AM, Asma rabe wrote:
> Hi All,
>
> When I tried BSgenome package for Hsapiens I got the output below. I wonder
> what are chromosomes other than chr1-chr22,chrX,Y and M.
> What is chr4_gl000193_random for instance.
>
> Thank you
> #=========
>
> Hsapiens
> Human genome
> |
> | organism: Homo sapiens (Human)
> | provider: UCSC
> | provider version: hg19
> | release date: Feb. 2009
> | release name: Genome Reference Consortium GRCh37
> |
> | single sequences (see '?seqnames'):
> |   chr1                   chr2                   chr3
> chr4                   chr5
> |   chr6                   chr7                   chr8
> chr9                   chr10
> |   chr11                  chr12                  chr13
>   chr14                  chr15
> |   chr16                  chr17                  chr18
>   chr19                  chr20
> |   chr21                  chr22                  chrX
> chrY                   chrM
> |   chr1_gl000191_random   chr1_gl000192_random   chr4_ctg9_hap1
> chr4_gl000193_random   chr4_gl000194_random
> |   chr6_apd_hap1          chr6_cox_hap2          chr6_dbb_hap3
>   chr6_mann_hap4         chr6_mcf_hap5
> |   chr6_qbl_hap6          chr6_ssto_hap7         chr7_gl000195_random
> chr8_gl000196_random   chr8_gl000197_random
> |   chr9_gl000198_random   chr9_gl000199_random   chr9_gl000200_random
> chr9_gl000201_random   chr11_gl000202_random
> |   chr17_ctg5_hap1        chr17_gl000203_random  chr17_gl000204_random
>   chr17_gl000205_random  chr17_gl000206_random
> |   chr18_gl000207_random  chr19_gl000208_random  chr19_gl000209_random
>   chr21_gl000210_random  chrUn_gl000211
> |   chrUn_gl000212         chrUn_gl000213         chrUn_gl000214
> chrUn_gl000215         chrUn_gl000216
> |   chrUn_gl000217         chrUn_gl000218         chrUn_gl000219
> chrUn_gl000220         chrUn_gl000221
> |   chrUn_gl000222         chrUn_gl000223         chrUn_gl000224
> chrUn_gl000225         chrUn_gl000226
> |   chrUn_gl000227         chrUn_gl000228         chrUn_gl000229
> chrUn_gl000230         chrUn_gl000231
> |   chrUn_gl000232         chrUn_gl000233         chrUn_gl000234
> chrUn_gl000235         chrUn_gl000236
> |   chrUn_gl000237         chrUn_gl000238         chrUn_gl000239
> chrUn_gl000240         chrUn_gl000241
> |   chrUn_gl000242         chrUn_gl000243         chrUn_gl000244
> chrUn_gl000245         chrUn_gl000246
> |   chrUn_gl000247         chrUn_gl000248         chrUn_gl000249
> |
> | multiple sequences (see '?mseqnames'):
> |   upstream1000  upstream2000  upstream5000
> |
> | (use the '$' or '[[' operator to access a given sequence)
>
> 	[[alternative HTML version deleted]]
>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099