Good Afternoon:
The genome sequences you mention are not available on the primary UCSC genome
browser
WEB site. You can obtain this information from the genome-preview browser.
Please try this script:
for G in vicPac1 dasNov2 papHam1 turTru1 pteVam1 myoLuc1 micMur1 ochPri2 \
proCap1 sorAra1 choHof1 tarSyr1 echTel1 macEug1
do
wget -O /dev/stdout \
"http://genome-preview.cse.ucsc.edu/cgi-bin/hgTables?submit=submit&hgta_doTopSubmit=1&hgta_table=chromInfo&hgta_outputType=primaryTable&hgta_regionType=genome&hgta_track=gold&db=${G}";
\
| grep -v "^#chrom" | cut -f1,2 | sort -k2,2nr > ${G}.chrom.sizes
echo "DONE: ${G}"
sleep 15
done
Please note the information about this type of procedure:
http://genomewiki.ucsc.edu/index.php/Table_Browser_URL
--Hiram
Guangyi Dai wrote:
> Dear UCSC,
>
> I'm trying to use Multiz to merge the pairwise alignments (all use human
> genome as a target) to get mutiple-species alignments. Before that, it is
> necessary for me to convert the axt format to maf format. So I need the
> tSizes and qSizes files of all the species I am interested.
>
> In the latest reply, Dr. Angie Hinrichs told us to use fetchChromSizes to get
> the sizes of different species. And it does work well in most species.
> However, fetchChromSizes still cannot get sizes of some species, such as
> aplaca_vicPac1, baboon_papHam1 and so on.
>
> As we can download the pairwise alignments (human genome as a target) of
> these species from UCSC, it should have been sequenced and have sizes files
> of all these species. So, I wonder where and how I can get these species'
> sizes files which cannot get by fetchChromSizes.
>
> We are looking forward to your reply. Thank you!
>
> PS: Here are the list of all these species lack sizes files.
>
> alpaca_vicPac1
> armadillo_dasNov2
> baboon_papHam1
> dolphin_turTru1
> megabat_pteVam1
> microbat_myoLuc1
> mouseLemur_micMur1
> pika_ochPri2
> rockHyrax_proCap1
> shrew_sorAra1
> sloth_choHof1
> tarsier_tarSyr1
> tenrec_echTel1
> wallaby_macEug1
>
>
> Guangyi Dai
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