Download alignmet from table browser

[Ruiz De Los Mozos, Igor]

Dear UCSC mainteinance,

I am trying to download several alignments and scores from the table browser conservation20way. I am using a bash script to do this, but I guess that my URL is not the adequate. I don't understand the cartDump step to get the CGI variables used on the query.

This is the script I'm using:

#!/bin/sh
POSITION="chr9:3A133252000-133280861"
wget --progress=dot \
'https://genome-euro.ucsc.edu/cgi-bin/hgTables?db=hg38&hgta_compressType=none&'\
'clade=mammal&'\
'org=Human&'\
'db=hg38&'\
'hgta_group=compGeno&'\
'hgta_track=cons20way&'\
'hgta_table=0&'\
'hgta_regionType=genome&'\
'position='${POSITION}\
'hgta_outputType=wigData&'\
'hgta_outFileName='${POSITION} \
'&submit=submit&hgta_doTopSubmit=1' \
    -O align_${POSITION}.cons

Any help will be much appreciated!! Thanks in advance, Igor

[Luvina Guruvadoo]

Hello Igor,

Thank you for your question. Your best option would be to extract this data using our hgWiggle utility, which you can download here: http://hgdownload.soe.ucsc.edu/admin/exe/. To access the data files, see our downloads server (scroll down to "Multiple Alignments"): http://hgdownload.soe.ucsc.edu/downloads.html#human

If you have any further questions, please reply to genome...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Regards,

Luvina

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Luvina Guruvadoo
UCSC Genome Browser
http://genome.ucsc.edu

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