FetchChromSizes
From BITS wiki
The FetchChromSizes script does at it says. It is provided by the UCSC team to download a chromosome list from the UCSC Table database and save it to a local text file. The script supports any genome present in the UCSC table database.
The unix version of the script can be downloaded in its current version from the following link [1].
# after download, the file should be made executable with chmod 0755 fetchChromSizes # downloading hg18 chromosome lengths is done with fetchChromSizes hg18 > hg18.chrom.sizes
result of the command
INFO: trying MySQL /usr/local/mysql/bin/mysql for database hg18 splaisan@stelap:~/Desktop$ cat hg18.chrom.sizes chr1 247249719 chr2 242951149 chr3 199501827 chr4 191273063 chr5 180857866 chr6 170899992 chr7 158821424 chrX 154913754 chr8 146274826 chr9 140273252 chr10 135374737 chr11 134452384 chr12 132349534 chr13 114142980 chr14 106368585 chr15 100338915 chr16 88827254 chr17 78774742 chr18 76117153 chr19 63811651 chr20 62435964 chrY 57772954 chr22 49691432 chr21 46944323 chr6_cox_hap1 4731698 chr6_qbl_hap2 4565931 chr17_random 2617613 chr6_random 1875562 chr5_h2_hap1 1794870 chrX_random 1719168 chr21_random 1679693 chr1_random 1663265 chr9_random 1146434 chr8_random 943810 chr4_random 842648 chr15_random 784346 chr3_random 749256 chr7_random 549659 chr19_random 301858 chr22_random 257318 chr11_random 215294 chr13_random 186858 chr2_random 185571 chr5_random 143687 chr10_random 113275 chr16_random 105485 chr22_h2_hap1 63661 chrM 16571 chr18_random 4262
References:
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