Download EST spliced alignments UCSC

Question

[Mariela Cortés-López]

Hi,

I would like to download the available EST alignments reported in the UCSC genome browser for a specific region. When I click a particular EST in the browser a new window appears with detailed information and the link "View details of parts of alignment within browser window", following that link there is a "side by side alignment", that is the particular section that I'm interested in, so I would like to know if there is any programmatically way to get that information without having to click on every single EST?

Thanks

Answer 1

[genecats.ucsc]

It is possible to generate those alignments with the pslPretty utility, available from our list of utilities:
http://hgdownload.soe.ucsc.edu/admin/exe

Here is an example where I also illustrate some other useful commands, faSomeRecords and pslSomeRecords, which are also available from the same directory listed above:

# download everything 
$ wget http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.2bit
$ wget http://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/all_est.txt.gz
$ wget http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/est.fa.gz

# format
$ gzip -cd all_est.txt.gz | cut -f2- > all_ext.psl
$ gzip -d est.fa.gz

# small example psl:
$ echo "BX437773" | pslSomeRecords all_ext.psl stdin onePsl.psl
$ echo "BX437773" | faSomeRecords est.fa stdin out.fa

# now run pslPretty
$ pslPretty onePsl.psl hg38.2bit out.fa pretty.out
$ cat pretty.out
>BX437773:0-883 of 897 chr1:11130551+11145019 of 248956422
gcgat-gggt-gggctgttctcgg.....75......cNNtggtggcgttgttctgttgN
||||| |||| |||||||||||||             |  ||||||||||| |    |  
GCGATGGGGTGGGGCTGTTCTCGG.....75......cagtggtggcgTTGGTGATGTTG

cccNgaaNggcctNccgccNatacttcttctc-NttNgcgggcttgNttctgatNtttNt
 ||     ||| |  |||   | |||||||||   | ||||||||| ||||||| ||| |
GCCCCGCTGGCATGACGCAGTTTCTTCTTCTCA--TCGCGGGCTTGGTTCTGATGTTTGT

NgtgtNgccccgattcgaagttcatcactgcccacgcatgccagNc-----2302-----
 |||| || | | ||||||||||||||||||||||||||||||| |              
AGTGTAGCACAGCTTCGAAGTTCATCACTGCCCACGCATGCCAGGCCTGGTT...GATCA
...
...
...

All 3 utils can be run with no arguments in order to get a usage message:

$ pslPretty 
pslPretty - Convert PSL to human-readable output
usage:
   pslPretty in.psl target.lst query.lst pretty.out
options:
   -axt             Save in format like Scott Schwartz's axt format.
                    Note gaps in both sequences are still allowed in the
                    output, which not all axt readers will expect.
   -dot=N           Output a dot every N records.
   -long            Don't abbreviate long inserts.
   -check=fileName  Output alignment checks to filename.
It's recommended that the psl file be sorted by target if it contains
multiple targets; otherwise, this will be extremely slow. The target and query
lists can be fasta, 2bit or nib files, or a list of these files, one per line.

If you have further questions about UCSC data or tools feel free to send your question to one of the below mailing lists:

• General questions: [e-mail]
• Questions involving private data: [e-mail]
• Questions involving mirror sites: [e-mail]

ChrisL from the UCSC Genome Browser