Command Builder

Even with our documentation, it may be tedious to construct the applicable commands and config file required to run majiq and voila manually. In order to help you get started with some basic use cases, we provide this quick-to-use interactive tool to help you create the appropriate sequence of commands for your use case.

Build commands:

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Quantify commands:

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Voila commands:

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What kind of analysis are you performing?

Comparison between two groups or more groups (e.g. WT vs. KO, No treatment vs drug1 vs drug2)

Quantification of multiple individual samples

How do you want PSI values to be calculated?

Group level PSI where replicates within a group from the build are quantified together

Individual sample PSI where every sample from every group is quantified separately

Is your dataset heterogeneous or well controlled?

Heterogeneous

Well controlled

Only show junctions that differ between groups by at least (in PSI)

Do you want to quantify intron retention?

Yes

No

Do you want to quantify de novo (unannotated) events?

Yes

No

In what fraction of samples (in %, or count) in a group do you want a junction to be quantifiable in order to appear in the results?

Default: 50%

% of experiments

or

experiments

How many samples do you need to believe a junction/intron is real enough to include for quantification (making your model more complex)?

%

Which junctions and introns are biologically relevant for your analysis? By relevant, we mean: junctions and introns must have at least X% PSI in at least Y% (or Z number) of samples per build group.

All junctions are relevant

How many threads do you want to use?

I don't know

Enter full path to the reference transcriptome annotation (in GFF3 format)

Enter full path to the directory containing your .bam and .bam.bai files.

Enter full path of directory where you want to output the splicegraph and majiq files

How many biological groups are you analyzing?

Enter the name of each group, followed by the list of samples for that group, separated by comma

Error: group names should only contain alphanumeric and underscore ("_") characters. You may consider using the following type of algorithm to automatically clean your group names if needed. (Python3)

                                      import re
                                      def clean_group_name(x):
                                        x = re.sub(r"[()`\[\]{}\"'<>]", "", x)
                                        x = re.sub(r"[^0-9a-zA-Z]+", "_", x)
                                        return x
                                      clean_group_name("«insert your name here»")