Read Length Distribution

Question: Read Length Distribution

6.7 years ago by

Hi, Is there a tool or easy way to obtain a read length distribution on a set of 454 reads in fasta format? I can't seem to find such a tool in Galaxy. Thank you, Elad

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modified 6.7 years ago by Jennifer Hillman Jackson ♦ 25k • written 6.7 years ago by Elad Firnberg • 20

6.7 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hi Elad, Start with the tool "FASTA manipulation -> Compute sequence length" to generate a length value for each sequence. Next, use "Statistics -> Summary Statistics for any numerical column" on the result to generate specific R function statistics (see the tool form for which and how to enter the expression). To visualize the distribution, use "Graph/Display Data -> Histogram of a numeric column". Hopefully this helps. Best, Jen Galaxy team

ADD COMMENT • link written 6.7 years ago by Jennifer Hillman Jackson ♦ 25k

6.7 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello, Other types of statistics can be generated with the "Join, Subtract and Group -> Group" tool, by adding an additional file manipulation. First run "Compute sequence length". Next run "Add column to an existing dataset" and set this to be the same value for all rows, "1" or something else simple. Nest, run "Group", with a group on the column containing the "Add column" value, and then click on "Add new Operation". Set "Type" to be "Mode" and "On column" to be the the sequence length. Very large files, usually when run with multiple operations, are occasionally to too large to run with this tool on the public main Galaxy instance. If this occurs, the first option is to simplify the query. If that doesn't work, then moving to a cloud instance would be the recommendation. Good luck with your project, Jen Galaxy team

ADD COMMENT • link written 6.7 years ago by Jennifer Hillman Jackson ♦ 25k

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