Length Of Genome Scaffolds In Ucsc Genome Browser

Question

[anuragm]

Is there a way to know the number of nucleotides(sequence length) of the different genome scaffolds that form the entire genome of the organism in the UCSC genome browser. For eg, the Xenopus genome in the database consists of 1596 different GLxxxxxx s, each upto 10^8 bp long. Is there a way to find out the number of bp corresponding to each such GL ?

Answer 1

[Pierre Lindenbaum]

download the data

$ curl -s "http://hgdownload.cse.ucsc.edu/goldenPath/xenTro3/database/chromInfo.txt.gz" | gunzip -c  | head
GL172637    7817814    /gbdb/xenTro3/xenTro3.2bit
GL172638    7803671    /gbdb/xenTro3/xenTro3.2bit
GL172639    7514772    /gbdb/xenTro3/xenTro3.2bit
GL172640    6577953    /gbdb/xenTro3/xenTro3.2bit
GL172641    6532643    /gbdb/xenTro3/xenTro3.2bit
GL172642    6423007    /gbdb/xenTro3/xenTro3.2bit
GL172643    5836443    /gbdb/xenTro3/xenTro3.2bit
GL172644    5732789    /gbdb/xenTro3/xenTro3.2bit
GL172645    5717149    /gbdb/xenTro3/xenTro3.2bit
GL172646    5704324    /gbdb/xenTro3/xenTro3.2bit

or use mysql:

$ mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -e 'select * from xenTro3.chromInfo' 
+----------+---------+----------------------------+
| chrom    | size    | fileName                   |
+----------+---------+----------------------------+
| GL172637 | 7817814 | /gbdb/xenTro3/xenTro3.2bit |
| GL172638 | 7803671 | /gbdb/xenTro3/xenTro3.2bit |
| GL172639 | 7514772 | /gbdb/xenTro3/xenTro3.2bit |
| GL172640 | 6577953 | /gbdb/xenTro3/xenTro3.2bit |
| GL172641 | 6532643 | /gbdb/xenTro3/xenTro3.2bit |
| GL172642 | 6423007 | /gbdb/xenTro3/xenTro3.2bit |
| GL172643 | 5836443 | /gbdb/xenTro3/xenTro3.2bit |
| GL172644 | 5732789 | /gbdb/xenTro3/xenTro3.2bit |
| GL172645 | 5717149 | /gbdb/xenTro3/xenTro3.2bit |
| GL172646 | 5704324 | /gbdb/xenTro3/xenTro3.2bit |