Performing Operations On Tab Delimited Text Files

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Question: Performing Operations On Tab Delimited Text Files

6.2 years ago by

Lanelle Oni Edwards • 50

Lanelle Oni Edwards • 50 wrote:

Hi, My name is Lanelle Edwards. I am a new galaxy user. I uploaded a tab delimited text file to my history. However, the first column of the data I imported is solely chromosome number and start and end position (ALL IN ONE COLUMN) in the format chrI:1000000-2000000. My question is: How can I filter out these values into separate columns using galaxy tools? For example: Having a separate column for chromosome number, column for start position, column for end position. I would really appreciate the help. Thanks, Lanelle Edwards Lab Manger University of Maryland

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modified 6.2 years ago by Jennifer Hillman Jackson ♦ 25k • written 6.2 years ago by Lanelle Oni Edwards • 50

6.2 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello Lanelle, A combination of text manipulations can extract the data into interval format. A good step-by-step example, including a video tutorial, is in the Using Galaxy paper & supplemental available here: http://main.g2.bx.psu.edu/u/galaxyproject/p/using-galaxy-2012 Protocol #2 has examples of loading 4 files - the 3rd file, starting with dataset #3, is the one where a column of data that combines chrom, start, stop is manipulated to produce distinct columns and assigned standard datatypes. This example has a ".." instead of a "-" between the start and stop, so just adjust that part of the manipulation to be specific for your data when you come to it. Hopefully this helps! Jen Galaxy team -- Jennifer Jackson http://galaxyproject.org

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