Hi

I downloaded the latest bsgenome...hg19. How many of the chromosomes have "N" as sequence.

however, chrM and others have regular letters.

Am I missing something here?

more information below

> library ("BSgenome.Hsapiens.UCSC.hg19")
> genome <- BSgenome.Hsapiens.UCSC.hg19
> genome$chr1
  249250621-letter "DNAString" instance
seq: NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN...NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

> genome$chrM
  16571-letter "DNAString" instance
seq: GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGAT...ACTGTATCCGACATCTGGTTCCTACTTCAGGGCCATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATG
> 
> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 8 x64 (build 9200)

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] BiocInstaller_1.18.4              BSgenome.Hsapiens.UCSC.hg19_1.4.0
 [3] BSgenome_1.36.3                   rtracklayer_1.28.10              
 [5] Biostrings_2.36.4                 XVector_0.8.0                    
 [7] GenomicRanges_1.20.6              GenomeInfoDb_1.4.2               
 [9] IRanges_2.2.7                     S4Vectors_0.6.5                  
[11] BiocGenerics_0.14.0              

loaded via a namespace (and not attached):
 [1] XML_3.98-1.3            Rsamtools_1.20.4        bitops_1.0-6           
 [4] GenomicAlignments_1.4.1 futile.options_1.0.0    zlibbioc_1.14.0        
 [7] futile.logger_1.4.1     lambda.r_1.1.7          BiocParallel_1.2.21    
[10] tools_3.2.2             RCurl_1.95-4.7         
> 

Most chromosomes start with many N's reflecting our imperfect knowledge of telomeres. Here you can see that the first 100 nucleotides are N , but the 100 nucleotides starting at position 100000 are not.

> which = GRanges("chr1", IRanges(c(1, 100000), width=100))
> getSeq(BSgenome.Hsapiens.UCSC.hg19, which)
  A DNAStringSet instance of length 2
    width seq
[1]   100 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN...NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
[2]   100 CACTAAGCACACAGAGAATAATGTCTAGAATCTG...GCAGTCACACAGGCTGACATGTAAGCATCGCCA