Most of the options available from the Galaxy interface to TAPDANCE are documented below.
This is the default view of TAPDANCE in galaxy after clicking the link in the tool bar. Each input item will be discussed below as well as any changes that may result in the view.
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The first choice a user is presented with is whether they would like to define the project parameters using Galaxy or whether to upload and use a predefined config file.
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There are three options for starting points in Galaxy, raw sequences, re-running a previous project or merging multiple existing projects.
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Choosing to start with sequences results in the following options.
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There is a default value for the mutagen sequence, but it is a fairly narrow range of experiments it will be useful for. TAPDANCE will attempt to match and strip the provided mutagen sequence(s) between the barcode and genomic sequence in the provided experimental sequences. Any experimental sequences that do not match a mutagen sequence are not used in subsequent steps of the TAPDANCE process.
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Entering a custom sequence and its relavent help text.
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Choose the reference genome for TAPDANCE to call Bowtie with for sequence alignment.
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When an existing project is the chosen starting point, the following options are available.
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Merging existing projects is very similar to re-running an existing project.
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To populate the list of projects to select from, the List TAPDANCE Projects tools needs to be invoked.
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The easiest route is to simply list all available projects.
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If the list of available projects is impractically long, using metadata tags to filter the list returned is useful. The returned list will only contain projects where at least one of the libraries had at least one of the tags entered on the form.
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If a predefined config file is used, the Galaxy interface has very few inputs to enter.
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The user has the choice of whether or not to call CIS on a project.
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In most cases, CIS will be called. This requires further input.
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Currently metadata describing the libraries is used in two ways. The first is to create subsets of libraries to call CIS on based on the metadata tags and the second is to aid in filtering projects later on in creating a list of projects to re-calculate or merge.
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With transposons local hopping can hopelessly clutter the area around the original site of the mutagen drowning out all signal with noise. Currently the remedy is to omit the chromosomes hosting the donor sites.
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A default set of features is provided, however it is unlikely to be suitable for many experiments. The default is here in the event that the user isn't all that interested in the CIS annotation and just wants the relevant intervals.
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Annotating CIS calls requires a BED file containing the features to annotate with.
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The default values for CIS calculation parameters should be reasonable, however the user does have the option to change them.
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The five CIS calling parameters start with their defaults when a user chooses to customize them.
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One of the few cases it makes sense to not go ahead and call CIS for a project is when a new set of data is being added for future merging with another project. If CIS calling is not needed, there are no further options to configure.
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