Question: Easiest Way To Obtain Chromosome Length?
12
gravatar for Sequer
7.4 years ago by
Sequer150
Malaysia
Sequer150 wrote:

Was just wondering contrary to a longer way. What is the easiest way for example to get a Drosophila melanogaster or any other organism's chromosome length?

length chromosome • 15k views
ADD COMMENTlink modified 4.4 years ago by Tommy Carstensen150 • written 7.4 years ago by Sequer150
13
gravatar for Pierre Lindenbaum
7.4 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum120k wrote:

As you cannot get the length of the longest chromosomes, I suppose that there is no such database.

The ucsc stores this information in the mysql table chromInfo for a few organisms.

$ mysql  --user=genome --host=genome-mysql.cse.ucsc.edu -A -D hg19 -e 'select chrom,size from chromInfo limit 5'
+-------+-----------+
| chrom | size      |
+-------+-----------+
| chr1  | 249250621 |
| chr2  | 243199373 |
| chr3  | 198022430 |
| chr4  | 191154276 |
| chr5  | 180915260 |
+-------+-----------+
ADD COMMENTlink written 7.4 years ago by Pierre Lindenbaum120k
11
gravatar for Casey Bergman
7.4 years ago by
Casey Bergman18k
Athens, GA, USA
Casey Bergman18k wrote:

The UCSC browser provides a summary page of chromosome lengths for each of the genomes in their database, e.g. for D. melanogaster (release 5/dm3): http://genome.ucsc.edu/cgi-bin/hgTracks?db=dm3&chromInfoPage=

Just swap the db=xx for another genome.

ADD COMMENTlink written 7.4 years ago by Casey Bergman18k
6
gravatar for Ian
7.4 years ago by
Ian5.5k
University of Manchester, UK
Ian5.5k wrote:

You can also use UCSCs fetchChromSizes script.

ADD COMMENTlink written 7.4 years ago by Ian5.5k

I knew their was a Kent utility to do this but couldn't find it this AM. Thanks Ian.

ADD REPLYlink written 7.4 years ago by Casey Bergman18k
2
gravatar for Gareth Palidwor
7.4 years ago by
Gareth Palidwor1.6k
Ottawa
Gareth Palidwor1.6k wrote:

Remember that the lengths you get from the model can have various biases. For example: there are 3 million N's added to each end of mouse and human assembly chromosomes (except chrY) to represent telomeres. These are conventions and not necessarily representative of "real" telomere length. This should be kept in mind when you're doing any sort of length related analysis.

ADD COMMENTlink modified 7.4 years ago • written 7.4 years ago by Gareth Palidwor1.6k

good point Gareth.

ADD REPLYlink written 7.4 years ago by Casey Bergman18k
0
gravatar for Tommy Carstensen
4.4 years ago by
United Kingdom
Tommy Carstensen150 wrote:

f your system doesn't have mysql as suggested by Pierre, then you can do (as suggested by Pierre in another thread):

curl -s ftp://hgdownload.cse.ucsc.edu/goldenPath/$db/database/chromInfo.txt.gz | gunzip -c

$db could for example be hg19:

curl -s ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/chromInfo.txt.gz | gunzip -c
ADD COMMENTlink modified 4.4 years ago • written 4.4 years ago by Tommy Carstensen150
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