Frequently Asked Questions

TABLE OF CONTENTS

1. How are the coordinates represented?
2. How are the regions listed in the browser display links?
3. What is the difference between tools and operations?
4. What is the difference between tools and displays?
5. How does the alignment retriever tool get the alignments for a query result?
6. What is the BED format or the extended BED format? How do I put blanks in these formats?
7. What is alignment stitching? What is the stitch file format?

1. How are the coordinates represented?

The result intervals stored at Galaxy are 0-based, half-open. The first basepair in the chromosome or contig is called "0". In each interval, the starting basepair is included, but the ending basepair is not. For example, the first 100 basepairs of chromosome 1 would be "chr1 0 100". This would include the basepairs numbered 0 through 99. However, most displays (except raw text outputs) will use 1-based, closed regions, where the chromosome starts at "1" and both endpoints are included.

2. How are the regions listed in the browser display links?

To help limit the length of the list while still displaying regions of manageable size, the results are grouped into chunks. Galaxy starts with the first region and gathers as many as it can until it reaches 100 kb. Then it ends that chunk (without splitting any regions) and starts the next. Finally it pads the chunks by 5% so that regions at the edges can be seen clearly.

3. What is the difference between tools and operations?

Operations are mathematically oriented, based only on regions' sizes and positions on the chromosome. Tools perform more complex, biologically-based computations or file format conversions.

4. What is the difference between tools and displays?

A tool will usually do some biological computations on the selected query, and always adds its results to the history page. Displays do not return any data to Galaxy; they just display their results directly. In both cases, the output can be either human-readable (e.g. a graph) or a computer-readable file.

5. How does the alignment retriever tool get the alignments for a query result?

The alignments are pre-computed. The tool will extract only the section of the alignment that is overlapped by a region in the query results. If there is no alignment at a result region, then nothing is returned for that region. If the alignment is larger than the region, only the portion of the alignment within the region is returned. If the alignment is smaller than the region then the whole alignment is returned, but the parts of the region that don't align are not represented.

6. What is the BED format or the extended BED format? How do I put blanks in these formats?

See UCSC standard BED format and Galaxy extended BED format.

7. What is alignment stitching? What is the stitch file format?

See Alignment stitching.