If I load the mouse mm10 genome, the names function gives me back 239 chromosomes:
> library("BSgenome.Mmusculus.UCSC.mm10")
> mouse <- BSgenome.Mmusculus.UCSC.mm10
> names(mouse)
[1] "chr1" "chr2" "chr3"
[4] "chr4" "chr5" "chr6"
[7] "chr7" "chr8" "chr9"
[10] "chr10" "chr11" "chr12"
[13] "chr13" "chr14" "chr15"
[16] "chr16" "chr17" "chr18"
[19] "chr19" "chrX" "chrY"
[22] "chrM" "chr1_GL455991_alt" "chr1_GL455992_alt"
[25] "chr1_GL455993_alt" "chr1_GL456005_alt" "chr1_JH584315_alt"
[28] "chr1_JH584320_alt" "chr1_JH584321_alt" "chr1_JH584322_alt"
[31] "chr2_GL456024_alt" "chr3_GL456006_alt" "chr3_GL456007_alt"
[34] "chr3_GL456008_alt" "chr3_GL456042_alt" "chr3_GL456044_alt"
[37] "chr3_GL456045_alt" "chr3_GL456048_alt" "chr3_GL456049_alt"
[40] "chr3_JH584323_alt" "chr4_GL455994_alt" "chr4_GL456009_alt"
[43] "chr4_GL456010_alt" "chr4_GL456053_alt" "chr4_GL456064_alt"
[46] "chr4_GL456075_alt" "chr4_GL456076_alt" "chr4_GL456077_alt"
[49] "chr4_JH584268_alt" "chr4_JH584269_alt" "chr4_JH584324_alt"
[52] "chr4_JH584325_alt" "chr4_JH584326_alt" "chr5_GL455995_alt"
[55] "chr5_GL456011_alt" "chr6_GL456012_alt" "chr6_GL456025_alt"
[58] "chr6_GL456026_alt" "chr6_GL456054_alt" "chr6_GL456065_alt"
[61] "chr6_JH584264_alt" "chr7_GL455989_alt" "chr7_GL456013_alt"
[64] "chr7_GL456014_alt" "chr8_GL455996_alt" "chr8_GL455997_alt"
[67] "chr10_GL456015_alt" "chr11_GL455998_alt" "chr11_GL456016_alt"
[70] "chr11_GL456060_alt" "chr11_JH584265_alt" "chr11_JH584316_alt"
[73] "chr11_JH584317_alt" "chr11_JH584327_alt" "chr12_GL456017_alt"
[76] "chr12_GL456068_alt" "chr12_GL456074_alt" "chr12_GL456078_alt"
[79] "chr12_GL456349_alt" "chr13_GL455990_alt" "chr13_GL455999_alt"
[82] "chr13_JH584305_alt" "chr14_GL456019_alt" "chr14_GL456020_alt"
[85] "chr15_GL456000_alt" "chr15_JH584270_alt" "chr16_GL456001_alt"
[88] "chr16_GL456028_alt" "chr16_JH584306_alt" "chr16_JH584307_alt"
[91] "chr16_JH584310_alt" "chr16_JH584311_alt" "chr16_JH584312_alt"
[94] "chr16_JH584313_alt" "chr16_JH584314_alt" "chr17_GL456002_alt"
[97] "chr17_GL456021_alt" "chr17_GL456022_alt" "chr17_GL456069_alt"
[100] "chr17_JH584266_alt" "chr17_JH584267_alt" "chr17_JH584308_alt"
[103] "chr17_JH584309_alt" "chr17_JH584328_alt" "chr17_JH590470_alt"
[106] "chr18_GL456070_alt" "chr18_JH584318_alt" "chr19_GL456079_alt"
[109] "chr19_JH584319_alt" "chrX_GL456003_alt" "chrX_GL456004_alt"
[112] "chrX_GL456031_alt" "chrX_GL456032_alt" "chrX_GL456033_alt"
[115] "chrY_GL456071_alt" "chrY_GL456072_alt" "chrY_GL456073_alt"
[118] "chrY_GL456080_alt" "chrY_GL456081_alt" "chrY_GL456082_alt"
[121] "chrna_GL456050_alt" "chr1_GL456210_random" "chr1_GL456211_random"
[124] "chr1_GL456212_random" "chr1_GL456213_random" "chr1_GL456221_random"
[127] "chr4_GL456216_random" "chr4_GL456350_random" "chr4_JH584292_random"
[130] "chr4_JH584293_random" "chr4_JH584294_random" "chr4_JH584295_random"
[133] "chr5_GL456354_random" "chr5_JH584296_random" "chr5_JH584297_random"
[136] "chr5_JH584298_random" "chr5_JH584299_random" "chr7_GL456219_random"
[139] "chrX_GL456233_random" "chrY_JH584300_random" "chrY_JH584301_random"
[142] "chrY_JH584302_random" "chrY_JH584303_random" "chrUn_GL456239"
[145] "chrUn_GL456359" "chrUn_GL456360" "chrUn_GL456366"
[148] "chrUn_GL456367" "chrUn_GL456368" "chrUn_GL456370"
[151] "chrUn_GL456372" "chrUn_GL456378" "chrUn_GL456379"
[154] "chrUn_GL456381" "chrUn_GL456382" "chrUn_GL456383"
[157] "chrUn_GL456385" "chrUn_GL456387" "chrUn_GL456389"
[160] "chrUn_GL456390" "chrUn_GL456392" "chrUn_GL456393"
[163] "chrUn_GL456394" "chrUn_GL456396" "chrUn_JH584304"
[166] "chr1_KV575232_fix" "chr1_KV575233_fix" "chr1_KV575234_fix"
[169] "chr2_KV575235_fix" "chr2_KV575236_fix" "chr3_KQ030484_fix"
[172] "chr3_KZ289064_fix" "chr3_KZ289065_fix" "chr3_KZ289066_fix"
[175] "chr4_JH792826_fix" "chr4_KQ030485_fix" "chr4_KQ030486_fix"
[178] "chr4_KQ030487_fix" "chr4_KQ030488_fix" "chr4_KQ030489_fix"
[181] "chr4_KZ289067_fix" "chr4_KZ289068_fix" "chr4_KZ289069_fix"
[184] "chr4_KZ289070_fix" "chr5_JH792827_fix" "chr5_KV575237_fix"
[187] "chr6_KK082442_fix" "chr6_KK082443_fix" "chr7_JH792828_fix"
[190] "chr7_KV575238_fix" "chr7_KV575239_fix" "chr8_KV575240_fix"
[193] "chr9_KB469738_fix" "chr9_KQ030490_fix" "chr10_KQ030491_fix"
[196] "chr10_KZ289071_fix" "chr10_KZ289072_fix" "chr11_KB469739_fix"
[199] "chr11_KZ289076_fix" "chr12_KB469740_fix" "chr12_KZ289082_fix"
[202] "chr14_KZ289083_fix" "chr14_KZ289084_fix" "chr15_KQ030492_fix"
[205] "chr15_KQ030493_fix" "chr15_KV575241_fix" "chr15_KZ289085_fix"
[208] "chr15_KZ289086_fix" "chr16_KB469741_fix" "chr17_KB469742_fix"
[211] "chr17_KZ289087_fix" "chr17_KZ289088_fix" "chr17_KZ289089_fix"
[214] "chr18_JH792829_fix" "chr18_KZ289090_fix" "chr18_KZ289091_fix"
[217] "chr19_JH792830_fix" "chr19_KQ030494_fix" "chr19_KV575242_fix"
[220] "chrX_JH792831_fix" "chrX_KQ030495_fix" "chrX_KQ030496_fix"
[223] "chrX_KQ030497_fix" "chrX_KZ289092_fix" "chrX_KZ289093_fix"
[226] "chrX_KZ289094_fix" "chrX_KZ289095_fix" "chrY_JH792832_fix"
[229] "chrY_JH792833_fix" "chrY_JH792834_fix" "chr1_KK082441_alt"
[232] "chr11_KZ289073_alt" "chr11_KZ289074_alt" "chr11_KZ289075_alt"
[235] "chr11_KZ289077_alt" "chr11_KZ289078_alt" "chr11_KZ289079_alt"
[238] "chr11_KZ289080_alt" "chr11_KZ289081_alt"
How is that possible? What if I don't need all these just the normal chr1-19 + chrX,Y,M? Can I get rid of the unnecessary ones?