WebReport^TM

WebReport gives the user access to a list of predefined reports which can be selected and downloaded for further data evaluation.

• Enter the project name and owner, or use the "Search" option to filter the full project list. The search option allows the user to search the full project list for the relevant project, with all or part of the project name. It is essential that both project name and owner are entered in WebReport as multiple projects with the same name may exist.
• StackPACK is not case-sensitive. Therefore, project names such as "UPPER" and "Upper" will be considered duplicates if they have the same owner.
• A window similar to the following will be displayed:



• Select the appropriate project name and corresponding project owner from the pop-up box.
• Upon clicking the "Select" button, the selected project details will be entered into WebReport as follows:



• Select the type of report you wish to generate by clicking the radio button next to your choice.
• Click on the "Next" button in order to select the options for the specified report.

A detailed description of each report is provided below:

All input sequences in masked or original FASTA format

• All project input sequences output to a single FASTA format file.
• The options window for this report is as follows:






• Masked: All masked input sequences output to a single FASTA format file.
• Original: All original or unmasked input sequences output to a single FASTA format file.
• The download is initialized by clicking on the "Export" button.

• Single FASTA file containing clonelinked consensus sequences, cluster primary consensus sequences or/and cluster alternate consensus sequences.
• The options window for this report is as follows:






• One or more of the consensus options may be selected simultaneously
• Clonelink Consensus Option: Single FASTA file containing all clonelinked consensus sequences as they appear in the Clonelink Consensus View.
• Primary Consensus Option: Single FASTA file containing the primary consensus sequence from each contig in every multi-sequence cluster, regardless of whether or not it is clonelinked. The header for each sequence will be the same as seen in the cluster Final Consensus View.
• Alternate Consensus Option: Single FASTA file containing all alternate consensus sequences from each contig in every multi-sequence cluster, regardless of whether or not it is clonelinked. The header for each sequence will be the same as seen in the cluster Final Consensus View.
• The download is initialized by clicking on the "Export" button.

• Single FASTA file containing singletons generated by d2_cluster or/and PHRAP.
• The options window for this report is as follows:






• Both singleton options may be selected simultaneously.
• Singletons: Single FASTA file containing all sequences not included by the clustering algoritm, d2_cluster, in multi-sequence clusters, as they appear in the EST or mRNA Sequence View.
• PHRAP Singletons: Single FASTA file containing all those sequences that were excluded from the PHRAP alignment, as they appear in the EST or mRNA Sequence View. These singletons are retained as cluster members.
• Minimum Sequence Length: A minimum sequence length to be output in base pairs may be specified. If no value is specified, the d2_cluster minimum_sequence_size parameter value is used by default. The default value for this parameter is 50 - sequences with less than 50 valid (A,T,C, and G) base pairs are ignored by d2_cluster and are thus not included in the clustering step. These sequences are considered singletons and are included in this report. The default parameter may be changed in the stackPACK configuration file when processing via the command line. Please see section 6, Expert Configuration, of the command line manual for further details.
• The download is initialized by clicking on the "Export" button.

• StackPACK is able to output both the initial PHRAP and final CRAW alignments into MSF and ClustalW formats, for further searching, editing and use in other programs. In addition, the PHRAP alignment can be outputted in old .ACE format for import into alignment editing programs such as Consed.
• The options window for this report is as follows:






• An accession number must be specified if the alignment for a particular cluster, contig or consensus is required. If omitted, all specified alignments for the project will be outputted.
• Cluster accession numbers (cl#) must be used when specifying ACE format. Only the initial PHRAP alignment can be output in ACE format. Sequence information will be output in the old ACE format.
• Contig accession numbers (ct#) must be specified when the PHRAP alignment is required.
• Consensus accession numbers (cn#) must be specified when the final alignment is required.


• The download is initialized by clicking on the "Export" button.

Note: PHRAP has limits of 64K bases for each sequence and 64K sequences per cluster. If these limits are exceeded within a cluster, a consensus sequence will not be generated for this cluster. Please refer to WebPipe for further details on how to overcome this.

• A single file containing the alignment analysis CRAW logs for multi-sequence clusters.
• The options window for this report is as follows:



• Contig (ct#) or cluster (cl#) accession numbers may be used to obtain the alignment analysis CRAW log for a particular contig or cluster.
• If the accession number is omitted, the alignment analyses for the whole project will be outputted.
• The download is initialized by clicking on the "Export" button.

• This selection produces a comprehensive non-redundant output report containing all data from the project.
• The options window for this report is as follows:






• FASTA Format:
  • The user is given the choice to select any or all of the following three options:
    • clonelinked consensus sequences
    • primary consensus sequences from multi-sequence clusters that are NOT found in clonelinked sequences
    • singleton sequences that are NOT found in clonelinked sequences.
  • The selection(s) are downloaded in a single FASTA-formatted output file. When all three items are selected, the most comprehensive, non-redundant report of output from stackPACK is generated.
  
  
• Comma Delimited:
  • This report is provided as an overview to the entire project that can easily be manipulated by the user.
  • All three options - clonelinked consensus sequences, primary consensus sequences and singletons - are provided by default.
  • All information about an EST or mRNA sequence is provided in a single row, including various stackPACK internal IDs, original EST or mRNA ID, length, clone library and clone ID information.
  • The resultant comma delimited file can be imported into most spreadsheet programs and sorted for further analysis.
  • NOTE: Microsoft Excel has a limit of 65,536 rows per worksheet. If your project has more than 65,536 sequences, you must first split the resulting .csv file, using a text editor or script, before attempting to open it. Other worksheet programs may have similar limits.
• The download is initialized by clicking on the "Export" button.

Note: Alternate consensus sequences are NOT included in the non-redundant output report.