Where can I download the length of short and long arms for each chromosome

Question

[zhao03]

Where can I download the length of short and long arm for each chromosome?

Thank you

Answer 1

[zx8754]

Download cytoband file from UCSC:

• http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/cytoBand.txt.gz

And summarise using R:

library(data.table)

x <- fread("http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/cytoBand.txt.gz", 
           col.names = c("chrom","chromStart","chromEnd","name","gieStain"))

x[ , .(length = sum(chromEnd - chromStart)), 
   by = .(chrom, arm = substring(name, 1, 1)) ]

#    chrom arm    length
# 1:  chr1   p 125000000
# 2:  chr1   q 124250621
# 3: chr10   p  40200000
# 4: chr10   q  95334747
# 5: chr11   p  53700000
# 6: chr11   q  81306516
# 7: chr12   p  35800000
# 8: chr12   q  98051895
# 9: chr13   p  17900000
#10: chr13   q  97269878
#11: chr14   p  17600000
#12: chr14   q  89749540
#13: chr15   p  19000000
#14: chr15   q  83531392
#15: chr16   p  36600000
#16: chr16   q  53754753
#17: chr17   p  24000000
#18: chr17   q  57195210
#19: chr18   p  17200000
#20: chr18   q  60877248
#21: chr19   p  26500000
#22: chr19   q  32628983
#23:  chr2   p  93300000
#24:  chr2   q 149899373
#25: chr20   p  27500000
#26: chr20   q  35525520
#27: chr21   p  13200000
#28: chr21   q  34929895
#29: chr22   p  14700000
#30: chr22   q  36604566
#31:  chr3   p  91000000
#32:  chr3   q 107022430
#33:  chr4   p  50400000
#34:  chr4   q 140754276
#35:  chr5   p  48400000
#36:  chr5   q 132515260
#37:  chr6   p  61000000
#38:  chr6   q 110115067
#39:  chr7   p  59900000
#40:  chr7   q  99238663
#41:  chr8   p  45600000
#42:  chr8   q 100764022
#43:  chr9   p  49000000
#44:  chr9   q  92213431
#45:  chrX   p  60600000
#46:  chrX   q  94670560
#47:  chrY   p  12500000
#48:  chrY   q  46873566
#    chrom arm    length

[Prakhar]

Just wanted to add a translation of this in tidyverse if that helps anyone:

arms_df <- read_tsv("http://hgdownload.cse.ucsc.edu/goldenpath/hg38/database/cytoBand.txt.gz", 
                    col_names = c("chrom","chromStart","chromEnd","name","gieStain")) |> 
           mutate(arm = substring(name, 1, 1)) |> 
           group_by(chrom, arm) |> 
           summarise(start_pos = min(chromStart),
                     end_pos = max(chromEnd),
                     length = end_pos - start_pos)

[archanaverma433]

How can I download the length of short and long arms for each chromosome of mouse? because when I did this -

 x <- fread("https://hgdownload.cse.ucsc.edu/goldenpath/mm10/database/cytoBand.txt.gz",
           col.names = c("chrom","chromStart","chromEnd","name","gieStain"))

 x[ , .(length = sum(chromEnd - chromStart)),
   by = .(chrom, arm = substring(name, 1, 1)) ]

 chrom arm    length
 1:  chr1   q 195471971
 2: chr10   q 130694993
 3: chr11   q 122082543
 4: chr12   q 120129022
 5: chr13   q 120421639
 6: chr14   q 124902244
 7: chr15   q 104043685
 8: chr16   q  98207768
 9: chr17   q  94987271
10: chr18   q  90702639
11: chr19   q  61431566
12:  chr2   q 182113224
13:  chr3   q 160039680
14:  chr4   q 156508116
15:  chr5   q 151834684
16:  chr6   q 149736546
17:  chr7   q 145441459
18:  chr8   q 129401213
19:  chr9   q 124595110
20:  chrX   q 171031299
21:  chrY   q  91744698
    chrom arm    length

I am getting only one arm length, Is this right ?

Thank you

[GenoMax]

From Jax Informatics:

The symbols p and q are used to denote the short and long arms, respectively, of mouse chromosomes. In translocations, breaks in the short arm should be designated with a p, but the q for long arm may be omitted if the meaning is clear. Because mouse autosomes and the X Chromosome are acrocentric, they do not have a short arm other than a telomere proximal to the centromere. Therefore, most rearrangements in mouse chromosomes involve breaks in the long arm (q arm). In mouse, Chr Y has both a p and q arm.

Answer 2

[GenoMax]

Table 4 contains the physical and genetic lengths of human chromosomes. I assumes that is what the question is about.