Hi Keith,

This does sound like a BED file format issue if that is your input type. A BED6 is necessary to capture strand. BED is different from Interval in that all columns are required to be in a specific order. In addition, all prior columns are required for later columns to be identified correctly. Practically, this means that at a minimum the first six fields must be defined for each line of your input. Use the Text Manipulation tools as needed to prepare the input.


For undefined values (if you do not have name or score), use placeholder values.
undefined name == a non-whitespace string
undefined score == "0"
(undefined strand == ".")

Below is the BED help from Convert Formats (to view in Galaxy, click on any that have a BED file as in/output).

Hopefully this helps, but if you continue to have trouble please feel free to share a history link and I can take a specific look at your data/result.

Best!
Jen
Galaxy team

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BED format Browser Extensible Data format was designed at UCSC for displaying data tracks in the Genome Browser. It has three required fields and several additional optional ones:

The first three BED fields (required) are:

1. chrom - The name of the chromosome (e.g. chr1, chrY_random).
2. chromStart - The starting position in the chromosome. (The first base in a chromosome is numbered 0.) 3. chromEnd - The ending position in the chromosome, plus 1 (i.e., a half-open interval).

The additional BED fields (optional) are:

 4. name - The name of the BED line.
 5. score - A score between 0 and 1000.
 6. strand - Defines the strand - either '+' or '-'.
7. thickStart - The starting position where the feature is drawn thickly at the Genome Browser. 8. thickEnd - The ending position where the feature is drawn thickly at the Genome Browser.
 9. reserved - This should always be set to zero.
10. blockCount - The number of blocks (exons) in the BED line.
11. blockSizes - A comma-separated list of the block sizes. The number of items in this list should correspond to blockCount. 12. blockStarts - A comma-separated list of block starts. All of the blockStart positions should be calculated relative to chromStart. The number of items in this list should correspond to blockCount.
13. expCount - The number of experiments.
14. expIds - A comma-separated list of experiment ids. The number of items in this list should correspond to expCount. 15. expScores - A comma-separated list of experiment scores. All of the expScores should be relative to expIds. The number of items in this list should correspond to expCount.




On 1/5/11 7:56 AM, Keith E. Giles wrote:
To be more specific, I continually get error's that say, NO records for
chromosome X (or any other), minus strand!

I just don't understand what the problem is here, because there are
millions of tags on each strand.  Could it be that the "-" characters is
not recognized by the MACS program so its ignoring all those tags?



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Jennifer Jackson
http://usegalaxy.org
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