Pipeline website: https://utap.wexac.weizmann.ac.il/
Information on 16.2.22 UTAP version history
A more comprehensive summary and guide to installing the system on your local cluster: https://utap.readthedocs.io
A guide for ChIP-seq and ATAC-seq pipelines: UTAP: ChIP-seq pipeline guidelines, UTAP: ATAC-seq pipeline guidelines
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UTAP is an intuitive and scalable transcriptome pipeline, which enables fast and user-friendly data analysis. The pipeline executes the full process, starting from sequences (RNA-Seq and bulk Mars-seq) and ending with sets of differentially expressed genes. Output files are placed in a structured folder system, and summarization of the results is displayed in a rich and comprehensive report.
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You may add additional categories by using the proper buttons:
If the samples were prepared in different batches, you can add this information: After the moving the samples into categories boxes, click on "Add Batch Effect" button, then select the samples that belongs to one batch and click on "Batch 1" button.
Return on the operation with the other groups of the samples.
All steps of the pipeline (mapping, counts etc.) will be run on all samples, but Deseq will be run only on the samples with categories.
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