Hello, For the first question, it is unclear what you mean. The files you list are the complete set of dm3 chromosomes when compared to the chromosome list on the dm3 gateway page (click through on the "Sequences" link).
Also declared on the gateway page are example search terms: chr2L Displays all of chromosome 2L chrYHet:1-200000 Displays first two hundred thousand bases of chromosome Y heterochromatin (a google search using "heterochromatin" brings up wiki definitions plus other links if you need some biology background for the term). The data comes from Berkeley Drosophila Genome Project (BDGP), as noted in the assembly credits. They performed the assembly and would be the appropriate people to contact concerning assembly details. http://www.fruitfly.org/ For the extra "bin" column in the hg19.refGene table/file - this is defined in the schema as "Indexing field to speed chromosome range queries". Some tables will have this and others will not. It can be ignored whenever found - the remainder of the table format will follow the data format spec. http://genome.ucsc.edu/FAQ/FAQformat.html Please let us know if your questions have not all been addressed, Jennifer --------------------------------- Jennifer Jackson UCSC Genome Informatics Group http://genome.ucsc.edu/ On 3/25/10 12:06 PM, Wang, Daqing wrote: > Dear Genome Assemblers, > > I didn't find the first chromosome sequence in drosophila (dm3) > chromFaMasked.tar.gz file as shown below. > In addition, what do 'LHet' and '2L' mean in files of chr2LHet.fa.masked and > chr2L.fa.masked ? > Another question, the RefGene file of rat (rn4) misses the first column as > compared to hu19.refGene, would you explain you have changed the format or > it's due to something else? You reply will be greatly appreciated ! > > tar xvf chromFaMasked.tar.gz > > -rw-rw-r-- 1 wangd3 bioinfo7 23471782 Jun 21 2007 chr2L.fa.masked > -rw-rw-r-- 1 wangd3 bioinfo7 376260 Jun 21 2007 chr2LHet.fa.masked > -rw-rw-r-- 1 wangd3 bioinfo7 21569650 Jun 21 2007 chr2R.fa.masked > -rw-rw-r-- 1 wangd3 bioinfo7 3354547 Jun 21 2007 chr2RHet.fa.masked > -rw-rw-r-- 1 wangd3 bioinfo7 25034436 Jun 21 2007 chr3L.fa.masked > -rw-rw-r-- 1 wangd3 bioinfo7 2606611 Jun 21 2007 chr3LHet.fa.masked > -rw-rw-r-- 1 wangd3 bioinfo7 28463162 Jun 21 2007 chr3R.fa.masked > -rw-rw-r-- 1 wangd3 bioinfo7 2567868 Jun 21 2007 chr3RHet.fa.masked > -rw-rw-r-- 1 wangd3 bioinfo7 1378901 Jun 21 2007 chr4.fa.masked > -rw-rw-r-- 1 wangd3 bioinfo7 19914 Jun 21 2007 chrM.fa.masked > -rw-rw-r-- 1 wangd3 bioinfo7 29584761 Jun 21 2007 chrUextra.fa.masked > -rw-rw-r-- 1 wangd3 bioinfo7 10250024 Jun 21 2007 chrU.fa.masked > -rw-rw-r-- 1 wangd3 bioinfo7 22871290 Jun 21 2007 chrX.fa.masked > -rw-rw-r-- 1 wangd3 bioinfo7 208204 Jun 21 2007 chrXHet.fa.masked > -rw-rw-r-- 1 wangd3 bioinfo7 353988 Jun 21 2007 chrYHet.fa.masked > > > Thanks, > > Daqing (Derek) Wang, PhD > Staff Scientist - Bioinformatics > > Life Technologies, Inc. > (Applied Biosystems) > Building 800 > Foster City, CA 94404 > > Office: (650) 638-5102 > E-mail: [email protected] > http://www.lifetechnologies.com/ > > ----------------------------- > > > > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
