bed files and GREAT

Question: bed files and GREAT

3.6 years ago by

sarai • 0

European Union

sarai • 0 wrote:

Hallow.

For chip-seq analysis, after MACS' I downloaded the BED file (produce by macs) and uploaded it in to GREAT (http://bejerano.stanford.edu/great/public-2.0.2/html/).

GREAT give me the following error message:

"GREAT encountered a user error.

GREAT encountered an error in your test set "Galaxy22-[chip-over-input_MACS_on_data_3_and_data_1_(peaks__bed)] (1).bed".

Please modify your data and re-submit it. If you need to report this error, please include this id: 20150413-public-2.0.2-3kZVyo

Error details:

Line 2: The fifth field (score) must be an integer (not 97.88). Input data: 'chr1 4420081 4421165 MACS_peak_1 97.88'

Line 3: The fifth field (score) must be an integer (not 53.47). Input data: 'chr1 4758155 4758796 MACS_peak_2 53.47'"

What am I doing wrong and how to fix it??

Thank you!

Sara.

bed files great • 1.1k views

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modified 3.6 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.6 years ago by sarai • 0

3.6 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello Sara,

If a tool requires that a input value is rounded, this can be manipulated in Galaxy before exporting. Tools in the group "Text manipulation" can be used to round values and then replace the old value with the new. The workflow will be something like:

1. input bed -> "Compute an expression on every row", using the column number of the score field (c5) as the expression and choosing to round the result

2. result of #1 -> "Cut columns from a table", to replace the old value with the new value added at the end of the row of each line (the rounded score).

For example, a bed dataset with 6 columns will have the new rounded value added as column 7. And the "Cut" replacement expression would be: "c1,c2,c3,c4,c7,c6" (do not use quotes on the tools form, and note that the original score value is omitted). If you are working with a bed dataset with more or less columns, or any tabular dataset, simply adjust the column numbers to match the original data, added fields, and what is wanted in the final file.

After manipulating with some of these tools, the dataset type will be output as "tabular". This is fine if you are downloading it, but if you want to use the data in Galaxy again as the original type, reassign it by clicking on the pencil icon.
http://wiki.galaxyproject.org/Support#Tabular.2FInterval.2FBED_Datatype_QA

Thanks, Jen, Galaxy team

ADD COMMENT • link modified 3.6 years ago • written 3.6 years ago by Jennifer Hillman Jackson ♦ 25k

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