getting sequence from multiz align track
VG
Matthew Speir
Thank you for your question about getting sequences from a Multiz
alignment in the UCSC Genome Browser.
You can get this information using the Table Browser. Here the steps you
would use to get this information from the 100-way Multiz alignment on hg38:
1. Navigate to the Table Browser, https://genome.ucsc.edu/cgi-bin/hgTables.
2. Make the following selections:
clade: Mammal
genome: Human
assembly: Dec. 2013 (GRCh38/hg38)
group: Comparative Genomics
track: Conservation
table: Multiz Align (multiz100way)
region: position or define a set of regions by clicking "define
regions"
output format: MAF - multiple alignment format
output file: enter a file name or leave blank to see results in the
browser
3. Click "get output".
Note that the results will include the alignment of all species in the
100-way alignment. If you output your results to a file, you can then
filter the species in the results using UNIX command line utilities such
as "grep".
I hope this is helpful. If you have any further questions, please reply
to gen...@soe.ucsc.edu. All messages sent to that address are archived
on a publicly-accessible Google Groups forum. If your question includes
sensitive data, you may send it instead to genom...@soe.ucsc.edu.
Matthew Speir
UCSC Genome Bioinformatics Group
>
VG
Jairo Navarro Gonzalez
Dear Varun,
Thank you for using the UCSC Genome Browser and your question about the MAF file formatting.
The reason you are seeing the MAF file broken into bases of 3, 18 and 5 is because of how the data is stored in the MAF file itself. The MAF blocks are broken whenever any one of the sequences changes orientation, chromosome, or position. If there are a lot of sequences in the alignment, the blocks can get really small. To learn more about MAF data files, please read our MAF format documentation.
I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a publicly-accessible Google Groups forum.
If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
Jairo Navarro
UCSC Genomics Institute
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VG
From: VG <gupta5...@gmail.com>
Date: Mon, May 1, 2017 at 3:40 PM
Subject: Re: [genome] getting sequence from multiz align track
To: Jairo Navarro Gonzalez <jnav...@ucsc.edu>
Jairo Navarro Gonzalez
Hello Varun,
If you output your results to a file, you can then filter the species in the results using UNIX command line utilities such as grep. For example, the following command should filter for only mouse and zebrafish:
grep "mm10\|danRer7" your_output_file
I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a publicly-accessible Google Groups forum.
If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
Jairo Navarro
UCSC Genomics Institute
To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/CAN7A_QyTeeoxPvATRXateznTog%3DWNpr%3DCCaMM%3D9UtHoDjUPzbw%40mail.gmail.com.