Outputs
SAW count is the main analysis pipeline to handle your FASTQs, usually with images. If you are not familiar with SAW analysis, the following will let you go through the basics of output files.
Where to find your output directory?
SAW count is performed under your work directory. Under the directory, a folder named by --id or --sn (with the absence of --id) will be found.
What are those in the output folder?
The output folder contains three parts:
/outs - main analysis output files, classified by data types.
/pipeline-logs - configuration of the analysis command and the pipeline log.
/STEREO_ANALYSIS_WORKFLOW_PROCESSING - intermediate datasets, statistic files, and module logs.
What are the main output files?
After the execution of SAW count , the output files are categorized by data types. Main output files are saved in /outs , so that it is convenient for analysts to find out what they want.
What is an HTML report?
The HTML report summarizes statistics and analysis results to present an overall picture of SAW count run. More interpretation of HTML report.
What is a visualization TAR file?
A compressed visualization TAR file integrates all the needed datasets for the analysis presentation in StereoMap, which includes expression matrices, analysis results and image-realted files.
How are the results different from SAW count?
SAW realign uses --count-data to obtain the results of read realignment, annotation, and the raw expression matrix. The manually processed image .tar.gz helps generate the expression matrices at tissue and cell dimensions, depending on the adjustments made to the image .tar.gz file.
Can I get an HTML from SAW realign?
Of course! You can restart the analysis with a processed image .tar.gz.
Access to help
Have any questions or concerns about the outputs of your SAW run?
Please get in touch with the local agents or FAS/FBS.
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