MGA - Search Page

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How to use the MGA-search page

This a short guide on how to use the search page in conjunction with the ChIP-Seq and SSA tools for exploring and analysing available data.

1. Search for a specific sample in the database

Searching for a sample / serie in the database is simple. Select the assembly you are intersted in and start typing in the 'sample name' field. As you type the input field will show a list of relevant samples. It is not necessary to select one of them since this is a free text search for any word. Be aware that different assemblies from the same organism might have different lists of samples / series.

Results are organised in Series showing the serie name, links to the serie documentation page in the MGA database and link to the publication. You can get a description of the serie if a question mark symbol is shown next to the serie name ([?]).

For each serie, the list of samples matching the search criteria shows the data type, sample name and three action buttons: the , and . The Hub will provide direct access to the sample data in SGA and BED format, and direct links to the ChIP-Seq and SSA tools for downstream analyses. Two ChIP-Seq tools (ChIP-Cor and ChIP-Extract) require the selection of a reference and a target feature. You can set them clicking on the relevant buttons. A new section in this page will show the selected features and direct links to the two tools. For an example describing how to set reference and target feature please go to point '4. Analysing data around genomic sites'.

2. Exporting sample data in BED format

To export data in BED format for a specific sample click on next to the sample name. This will open the sample Hub in a new page where the data can be downloaded in SGA or BED format. Data can also be lifted over to other asseblies.

3. Generating a peak list for a selected sample

Peak finding is done with the ChIP-Seq tool ChIP-Peak. To load search results in ChIP-Peak click on next to the sample name. The sample Hub page will show a list of available downstream analysis tools. Click on to go to ChIP-Peak. More information about the use of ChIP-Peak can be found in section 2 of this tutorial.

4. Analysing data around genomic sites

5. Heatmaps and data downlad for selected regions

6. Making a UCSC custom track for selected regions

Last update August 2017