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Question: How to convert SAM file to tabular ??
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gravatar for felipe_o_torquato
2.2 years ago by
felipe_o_torquato • 10
felipe_o_torquato • 10 wrote:

Hi everyone,

I am trying to convert the SAM file to tabular ?? Does anybody know?

Is there any way to open SAM file in excel?

many thanks in advance
convert format excel sam tabular • 2.0k views
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modified 2.2 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.2 years ago by felipe_o_torquato • 10
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gravatar for Jennifer Hillman Jackson
2.2 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

SAM datasets are already in tabular format. SAM is a more specific datatype assignment (header and column metadata is recognized).

Many tools that accept tabular format within Galaxy will accept SAM format directly. Others will require that the header is removed first. And certain others will require that both the header is removed and the datatype assignment is changed to be "tabular".

If the header is removed and the dataset is downloaded, it can be imported into Excel on your local computer as tabular data. If needed, change the file extension after downloaded to be ".txt" and make sure Excel knows that the imported data is in tabular format (not csv, etc).

To remove the header, there are a few options. These are the most direct:

  • Text Manipulation > Remove beginning of a file where the number of lines is equal to the number of lines in the header.
  • Filter and Sort > Select with the option NOT matching and the expression ^@

To change the datatype:

Best, Jen, Galaxy team
ADD COMMENT • link written 2.2 years ago by Jennifer Hillman Jackson ♦ 25k
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