Culture and Ecology of Chaco Canyon and the San Juan Basin

Output File Types 115Intensity FilesMain SequenceFiles from BustardOptional Files fromBustardThe prefix of the intensity filenames follows the prefix of the image filenames,but the tile position is padded to four digits. For example, s_1_0006_int.txt isthe intensity file corresponding to the image files s_1_6_a.tif, s_1_6_c.tif, andso on.Each intensity file has a set of data for remapped clusters on each line. Eachrow corresponds to the data from one cluster and each column is delimitedby a space. Each row has a lane index, and a tile index in the first column,with the X offset and Y offset of the cluster in the second and third columns(all coordinates indexed from zero). These fields are tab-delimited. Thesevalues should be enough to uniquely identify any cluster for any run.Following the coordinate fields are the data fields. The first value in a datafield is the raw intensity for base A, the second is the raw intensity for base C,then G, and then T. These four values are separated by spaces and arefollowed by a tab to mark the beginning of the next four values. The nextfour values represent the corresponding intensities in the de-block scan (if ade-block scan has been performed), and then four intensities for the nextcycle.The number of fields should equal four coordinates plus four bases times thenumber of cycles of processed data, even if clusters don't yield data at theend of a set of cycles or part way through. In this case, the fields contain 0.0and preserve delimiters.The following is a sample line from an intensity file (_int.txt): \... A second set of files with an identical layout, stores the estimates of the noiseon the intensity estimates. These files end in _nse.txt.The main output files in Bustard are the _qseq files. They have the followingformat: Machine name: (hopefully) unique identifier of the sequencer. Run number: (hopefully) unique number to identify the run on thesequencer. Lane number: positive integer (currently 1-8). Tile number: positive integer. X: x coordinate of the spot. Integer (can be negative). Y: y coordinate of the spot. Integer (can be negative). Index: positive integer. No indexing should have a value of 1. Read Number: 1 for single reads; 1 or 2 for paired ends. Sequence Quality: the calibrated quality string. Filter: Did the read pass filtering? 0 - No, 1 - Yes.Sequence FilesThe data found in the sequence files (_seq.txt) located in the Bustard folderare raw sequences in the following condition:Genome Analyzer Pipeline v1.3 and CASAVA v1.0 Software User Guide