File Setup Wizard

Organising the Data

This wizard is used to build the file hierarchy that describes the original wet lab experiment similar to the image shown below.

An Example of a File Hierarchy consisting of three samples with two replicates each
An Example of a File Hierarchy consisting of three samples with two replicates each

Users should first setup their samples in Step 1. By either giving the new sample a name by entering it into the indicated box and pressing the add sample button, alternatively if this field is left blank a name will be automatically generated.

Next users must move to Step 2 configure the references to be used. This will include a mandatory genome

Genome setup options. Users can select to map with patman or bowtie
Genome setup options. Users can select to map with patman or bowtie

The sequence alignment can be either handled with PatMan [1] or Bowtie [2]. If Bowtie is required users must supply the first filename in a set of pre-indexed genome files (genome pre-indexes can be found on the Bowtie website)

Following this, users can either choose to finish setup here, or supply an additional GFF file that will be used to annotate the sequences found in the sample files.

Users have the option to provide a GFF file for annotating sequences
Users have the option to provide a GFF file for annotating sequences

After a GFF file is specified users should move to Step 3 and select the annotations they wish to include in their result sets (The more annotations selected, the more work the software must do.)

Users are shown a list of all annotation types discovered in their GFF file. A tooltip gives the exact amount of transcripts found for that annotation
Users are shown a list of all annotation types discovered in their GFF file. A tooltip gives the exact amount of transcripts found for that annotation

Users can drag each annotation into either the ‘selected’ list or the ‘other’ list. Any annotations in the ‘selected’ list will be treated individually, those in the ‘other’ list will be grouped together and referred to as ‘other’ in any further analysis

Users drag the required annotation into either the selected or other list to have this annotation considered further downstream
Users drag the required annotation into either the selected or other list to have this annotation considered further downstream

 

[1] K. Prufer, U. Stenzel, M. Dannemann, R. E. Green, M. Lachmann, and J. Kelso, “PatMaN: rapid alignment of short sequences to large databases.,” Bioinformatics, vol. 24, no. 13, pp. 1530–1531, Jul. 2008.

[2] B. Langmead, C. Trapnell, M. Pop, and S. L. Salzberg, “Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.,” Genome Biol., vol. 10, no. 3, p. R25, Jan. 2009.

A suite of tools for analysing micro RNA and other small RNA data from High-Throughput Sequencing devices