• Dataset is one of the following: (1) A file of sequences with optional count data from conditions, where the sequences can be nucleotide or amino acid. (2) A set of sequences to assemble, with optional quality data.
• Conditions may be tissues, treatments, etc that are to be compared, with optional replicates.
• AnnoDBs are FASTA files of sequences (nucleotide or amino acid) to compare the dataset sequences against for annotation. TCW provides special support for UniProt, but can use any file of sequences (e.g. Genbank nr), see runAS for obtaining and formatting the files.
• NT-sTCWdb is a database built with nucleotide sequences. AA-sTCWdb is a database built with amino acid sequences.

Contents

• Running the demo -- Highly recommended to do this first
   
• Creating a new project
  1. Build Database
     • Input files
     • Entering sequence dataset
     • Updating attributes
     • Defining count data
       • Biological replicates
       • The count file
     
     
  2. Instantiate (optional Assembly)
      
  3. Annotation
     • AnnoDBs and UniProt
       • Options panel
     • GO annotation (also InterPro, EC, Pfam, KEGG)
     • ORF finder
     • Similar pairs
     • Adding to annotation
     • Adding remarks and locations
     • Remove...
     • Trouble shooting
     
     
  4. Differential Expression
  
  
• Important details
  • Directory structure and configuration files
  • Batch processing
  
  
• View/Query (viewSingleTCW)

The following three demos are supplied with the package to test runSingleTCW:

At the command line, type

   ./runSingleTCW

The window shown on the right will be launched. Select demoTra from the Project drop-down list. →A command button will turn inactive while it is executing, and there will be output to the terminal with any errors, warning and the state of execution. →A command button will be inactive when it is not valid to run, e.g. the Instantiate command inactive since the datasets have not been loaded.

1. Click the Step 1. Build Database button.
This loads the datasets in this section; there is one dataset of transcripts with count data for three conditions ("Stem","Root","OLeaf"), with five replicates each.

2. Click the Step 2. Instantiate button.

• The Skip Assembly was checked so the transcripts will simply be loaded, without assembly.
• The Use Sequence Names From File is not checked, meaning that the TCW will assign new, sequentially-numbered names prefixed by the singleTCW ID.

From this point on, you may Launch viewSingleTCW or select the Overview button to check status.

3. Click the Step 3. Annotate button.
This searches against several UniProt partial databases which have been provided as part of the package.

There may be one or more prompts for you to answer at the terminal; keep an eye on the terminal until it says "Start annotating sequences", at which point, it will run without any further prompts. For example, if the GO database has not been built yet (see Step 5), the following will be written to the terminal:

   +++Warning: GO_tree go_demo is missing; ignoring GO step
   --Please confirm above parameters. Continue with annotation?  (y/n)?

Log file: The output to the terminal and to the file projects/demoTra/logs/anno.log will look something like this log (this includes the GO annotation).

4. Click the Add Remarks or Location button (bottom of window), a window will popup (not shown).

1. Select the "..." on the same line as the label Location file:, select the file "traLocations.txt", then select the button Add on the same line.
2. Select the "..." on the same line as the label Remark file:, select the file "traRemarks.txt", then select the button Add on the same line.

5. To build the GO database, see Demo annotation setup. Then execute GO Only.

Time for adding the GOs: This take longer than the other TCW steps, where it can takes around 2 to 5 minutes for this demo. If it takes a lot longer than 4 minutes for this step, check your max_allows_packet (see Trouble shooting).

6. To compute differential expression (DE), install R and the respective packages. From the command line, execute

   ./runDE tra

Overview: See overview for the final demoTra overview from the above 6 steps.

7. (Optional) Add non-UniProt annoDBs

Back on the main window, select Check All then UnCheck All, which unchecks all current annoDB entries. Select Import AnnoDBs, then select file AnnoDBs_other.cfg. The AnnoDB table will look like the figure below.

• GOs: If you add more UniProt databases, you will want to redo GO. But since none of these annoDBs have GOs, the GO computation does not need to be redone; on the Options panel, select Ignore on Annotate (the "GO: go_demo (Ign)" text in the image above indicates this has been set).
• Pairs: if you had previously computed pairs, go to Options and unselect this option.
• Select Annotate.

   ?--Annotation exists in database. Enter [a/d/e]
    Add to existing annotation [a], Delete annotation [d], Exit [e]: a

Before starting, follow the steps of Installation. Make sure your HOSTS.cfg is correct.

To create a new project, press the Add Project button at the top of the runSingleTCW interface. You will be prompted for a project name; enter a name using letters, numbers, or underscores (no spaces). When you select "OK", the following occurs: The "name" will be entered for singleTCW ID and "sTCW_<name>" will be entered for the Database. The project/<name> directory will be created with files LIB.cfg and sTCW.cfg. These maintain all information you enter.

singleTCW ID: This should be a short descriptive name (2-5 characters, e.g. "ex"). It is used for the following:

1. This can be used as a command line parameter to runDE and viewSingleTCW, e.g. "viewSingleTCW ex".
2. If TCW generates the sequence names (if Use Sequence Names from File is not checked), the singleTCW ID followed by sequential numbers will be used, e.g. ex_00001, ex_00002, etc.

Instead of using the Add Projects, you may create a directory under /projects and put your sequence files along with any other optional files (i.e. quality and count); when you select the project pulldown, you will see your project (the project pulldown lists all directories under /projects).

Input files

1. Sequence and count files

The sequence names in the count file must match the sequence names in the sequence file. The count file is a tab or space delimited file. The first line of the count file is the heading "SeqID" (or any label) followed by the replicate names. The replicate names should end in the replicate number, e.g.

   SeqID	Leaf1	Leaf2	Leaf3	Root1	Root2	Root3

The conditions will be displayed in viewSingleTCW in the same order as the input.

2. Sequence and quality files

3. Multiple sequence files

Entering a sequence dataset

A TCW project must have at least one sequence dataset, which is a FASTA file of sequences. Select Add beside the Sequence Datasets and the panel will be replaced with the one shown on the lower right.

SeqID: Enter the dataset name (a brief identifier) in the first box; it should be a short (3-5 characters) name. (This SeqID is not dependent on the sequence names in the input files). Sequence File: Click the browse button labeled "..." to select the FASTA file of sequences. Additional information: Count File: For already assembled transcripts (e.g. Illumina) or protein sequences, there may be associated count files. Adding them is covered below in Defining count data.   ATTRIBUTES: Enter any additional information as desired in this section. This information is very important as it provides a description of the data that is stored in the database and shown on the Overview panel of viewSingleTCW.

• Quality File: For Sanger ESTs or 454 data, there may be a quality file (standard Phred quality scores in FASTA format).
• Sanger ESTs: TCW assumes the 5' ESTs have the ".f" suffix and the 3' ESTs have the ".r" suffix. If there are different from this, enter the correct ones.

After entering the files and attributes, select Keep. The main panel will reappear with the SeqID and Title added to the Sequence Datasets table. Additionally, the information will be written in projects/<name>/LIB.cfg.

Define all datasets, then select Build Database to load the data into the database. Datasets cannot be added to an existing database.

Updating attributes

Count File: Click the browse button labeled "..." to select the file containing the table of counts for the sequences. Alternatively, you can build the combined count file from multiple files, as described in Build from multiple count files. When Keep is selected at the bottom of this window (not shown), the dataset panel disappears and the main panel returns.

The panel shown on the right is part of the main panel. The sequence dataset will be shown in the first table, while the conditions (column headings from the count file) will be listed in the second table. Use Define Replicates to group replicates, as discussed in the next section. After defining the replicates, use Edit Attributes to add information for the conditions, which will be shown on the viewSingleTCW overview.

If you have biological replicates, you now need to click Define Replicates to define them. This brings up the panel shown on the right (example data from "demoTra"). The first column shows the sequence SeqID, which you entered when creating the sequence dataset. The second column shows the "Column name from file", which are the column headers in the count file (see example below). The third column shows the "Condition", which groups the replicates into a single condition. If the replicates names in the count file are named with the format "condition name + replicate number" (e.g. Root1), then TCW can automatically group them correctly.

Otherwise, you will need to edit the "Condition" column to map your replicate names to their condition. To edit a "Condition", highlight the row, then click on the appropriate cell (it is a little finicky, you may need to click at the beginning or end or double click...); it will turn white indicating you can edit the cell.

On Keep, the Associated Counts table on the main panel will be updated, showing the correct condition list and number of replicates for each (as shown on the right). In order to add metadata (e.g. title), select a row followed by Edit.

Naming rules:

1. There must not be any duplicate names between the SeqID column of the first table and the Condition of the second table, e.g. there may not be a SeqID of "Root" in this example.
2. There can be NO duplicate replicate or condition names between Sequence Datasets.

Example Count File: The following is the demoTra count file, showing the first 4 transcripts and counts for three conditions, where there is 3 conditions(tissues) with 5 replicates each. TCW determines the condition names and replicate numbers are from the column headers. The sequence names must correspond to those in the sequence file.

  SeqID    Stem1   Stem2  Stem3  Stem4  Stem5  Root1  Root2  Root3  Root4  Root5  Oleaf1 Oleaf2 Oleaf3 Oleaf4 Oleaf5
  tZoR_002048  556   572    766    770    777    294    361    291    300    399    264    173    162    407    382
  tZoR_147465  1172  1965   1009   1110   2245   10     425    593    251    347    1542   880    1648   3043   1024
  tZoR_108557  51    52     73     41     49     2      131    64     70     108    0      10     5      5      10
  tZoR_118798  52    51     35     37     33     1      69     138    61     134    8      9      7      21     6

Build from multiple count files

The easiest way to handle many sample files is to put them in one directory. Name each file with the "condition name + replicate number"; TCW parses up to the first "." to determine the condition and replicate number (the suffix can be whatever you want). For example, in the directory projects/demoTra/counts are the files:

   Root1.cnt   Root2.cnt   Root3.cnt   Root4.cnt   Root5.cnt
   Tip1.cnt    Zone1.cnt

To build the file, select Build from multiple count file from the Add or Edit a Sequence Dataset panel.

From the resulting panel, elect Add Directory of Files, which brings up a file chooser window; select the directory containing the files (e.g. "count") and it loads all files from the selected directory, as shown on the right. The file prefix (e.g. Root1) is shown in the "Rep name" column, and is used as the column heading in the combined file. Furthermore, the replicates for a condition will be grouped together by the text up to the number (as shown previously in Define biological replicates). Select Generate File to build the file called Combined_read_counts.csv. Control will return to the Sequence Dataset panel, and this filename will be automatically entered into the "Count File:" entry box.

If your files are not in one directory, or not named correctly, you will need to add them individually using the Add Rep File. You probably will need to edit the "Rep name" column; to edit the name, highlight the row then click the mouse at the right edge of the entry box (if that doesn't work, trying clicking at the beginning).

As already described, the replicates are grouped by clicking the Define Replicates button on the main window.

Skip Assembly: If the input is already assembled transcript sequences, or protein sequences, or gene sequences, check this option. If the datasets are ESTs, or multiple transcript datasets that you want to assemble together, do not select this option and see Assembly Guide.

Press Instantiate to either assemble or finalize the sequences in the database.

Use Sequence Names from File: If the sequences are NOT going to be assembled, then this checkbox is relevant, as follows: If you want TCW to name the sequences, do not check this option; TCW will rename the sequences using the SingleTCW ID followed by sequential numbers. If you want to use the original names from file, check this option; note the following restrictions:

• Characters other than letters, numbers, or underscores will be replaced by underscores.
• The names must be under 25 characters. Note that the names supplied by sequencers are often longer than allowed, which will make this fail.

1. Compares one or more protein and/or nucleotide databases ("annoDBs") to each sequence in the database. If the annoDBs are from UniProt, add the associated GO annotations.
2. Compute GC content and ORFs, where the ORF computation uses the functional annotation.
3. Compute pairs of similar sequences within the input set.

The Import AnnoDBs button (shown below) provides a way to enter all UniProt databases at once. If you used runAS for the annotation setup, make sure the last step was to select the AnnoDBs.cfg button, which creates a file of UniProt databases.

Select Import AnnoDBs, which pops up a file chooser, then select the file projects/AnnoDBs_UniProt_<date> (or sTCW.cfg of another project); all your UniProts will be added at once.

Taxonomy: This does not need to be unique, but the Annodb ID must be. Annodb ID is DBtype+taxonomy. The DBtype is read from the file (see Creating AnnoDBs). For example, if the DBtype is 'sp' (SwissProt) and the taxonomy is 'plants', the AnnoDB ID will be "SPpla". The AnnoDB ID is shown in various tables of viewSingleTCW to indicate the origin of the hit.

Generate Hit Tabular File:

Search Program: Select DIAMOND or BLAST.

Parameters: Defaults will be provided based on the search program selected, which can be changed.

Use Existing Hit Tabular File:

You can supply your own hit results file (must be in tabular format). You must still provide the annoDB FASTA file as it extracts the description and species from it.

The Options button below the AnnoDBs table provides additional options, as shown in the panel on the right. There are sections for ANNOTATION, ORF FINDER, and SIMILAR PAIRS. The second option and part of the third are not available for TCW database created from protein sequences.

ANNOTATIONS:

Remove {ECO...} from UniProt descripts: Most UniProt descriptions have {ECO...} text, e.g.

   >sp|A0A096SRM5|708A6_MAIZE UDP-glycosyltransferase 708A6 {ECO:0000303|PubMed:24045947}

Prune hits: See the Annotation Guide Prune Hits section for a details discussion. The options are:

GC content and ORF finding is always performed when Annotate is performed. The ORF finder uses the annoDB hits to aid in determining the best open reading frame.

SIMILAR PAIRS:

More information is provided in the Help page of the Options panel.

Adding to annotation

Select the Add Remarks or Locations button at the bottom of the runSingleTCW panel; the panel on the right will replace the main panel. Details of each function is provided below. Both the locations and remarks can be search and viewed in viewSingleTCW. Remarks are a very good way to add additional information to the sequences.

Add Location File

The file is a set of rows where the first word of each row is the sequence name and the rest of the row is the format:

   group:start-end(strand), e.g. SC_1:392-496(-)

A script is available, scripts/extractCodingLoc.pl, to generate the transcript sequence file from a genome sequence and GFF3 file. It also generates the location file in the format needed by TCW. It only works with a subset of the GFF3 files, so probably needs to be modified for your GFF3 or GTF file. It uses BioPerl.

The group name, start, end and strand are columns in the TCW database that can be viewed in viewSingleTCW by selecting the "Columns" tab on the left, then checking the columns under "General".

Add Remark File

The file is a set of rows where the first word of each row is the sequence name and the rest of the row is the Remark.

• Single and double quotes will be changed to spaces.
• Semi-colon will be changed to a colon.

In viewSingleTCW, the User Remark can be viewed by selecting the Columns tab, then checking the User Remark column under General. The remark can also be search on in the Basic Filters Sequence; this is a great way to add additional information about your sequences. If you make the remarks "keyword=value", you can then search on the keyword to get a specific group of sequences.

Remove Remarks

The image on the right shows what can be removed. The checked items are useful for redoing parts of the annotation, as discussed in Annotate Guide Update and Redo annotation section.

If the information on the runSingleTCW panel does not look right, remove /projects/<project>/LIB.cfg to start over. You can try fixing the problem by editing this file, but it is important to format it correctly. If that does not work, email tcw@agcol.arizona.edu and we will guide you on how to enter the information.

If you have many sequences (e.g. transcripts) in the database and/or many annoDBs, this can take a lot of memory. Running Annotate sets the memory to 8192, which may not be enough; in this case, once runSingleTCW is ready to annotate your database, exit and run from the command line:

   ./execAnno <project>

Also see Trouble shooting.

For full details on the DE computation, see the Differential Expression Guide.

IMPORTANT DETAILS

When a project is added with Add Project, runSingleTCW creates a directory under /projects with the user supplied name (referred to here as <project>). The projects/<project> directory has a LIB.cfg file where runSingleTCW saves all the library information and a sTCW.cfg file where runSingleTCW saves all the assembly and annotation information.

Though you can put your data files anywhere that runSingleTCW can access, you may want to put your data files in the projects/<project> directory in order to keep everything in one place. Also, the /DBfasta directory contains a subset of the UniProt files for the demo; this is a good location to put all annoDB files.

The three major steps write to the projects/<project> directory. The Annotate step puts all hit results in hitResults subdirectory. Hit files are NOT removed as they may be reused.

Each command line script takes as input the <project> name, along with some optional flags; execute the script followed by -h to see the flags (e.g. ./execAnno -h). All three take as input the "-n", which suppresses any prompts and uses defaults (as described by -h); this is good for batch processing.

The instantiation (or assembly) computed TPM (transcripts per kilobase per million); in order to compute the RPKM instead, execute:

   ./execAssm <project> -r

1. From the command line (./viewSingleTCW), which brings up a panel of mySQL databases with the sTCW_ prefix, where databases can be selected to view.
2. From the command line using the singleTCW ID or sTCW Database as a parameter (e.g. viewSingleTCW tra).
3. Through the button at the bottom of the Manager interface (Fig. 1).