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Download and install the UGENE FULL or NGS package to use this pipeline. |
Use this workflow sample to process raw RNA-seq next-generation sequencing (NGS) data from the Illumina platform. The processing includes:
- Filtration:
- Filtering of the NGS short reads by the CASAVA 1.8 header;
- Trimming of the short reads by quality;
- [Optionally] Mapping:
- Mapping of the short reads to the specified reference sequence (the TopHat tool is used in the sample);
The result output of the workflow contains the filtered and merged FASTQ files. In case the TopHat mapping has been done, the result also contains the TopHat output files: the accepted hits BAM file and tracks of junctions, insertions and deletions in BED format. Other intermediate data files are also output by the workflow.
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If you haven't used the workflow samples in UGENE before, look at the "How to Use Sample Workflows" section of the documentation. |
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The Tuxedo workflow can be used to analyze the filtered RNA-seq data. In this case the mapping step of this workflow can be skipped, as it also present in the Tuxedo pipeline. |
Workflow Sample Location
The workflow sample "Raw DNA-Seq processing" can be found in the "NGS" section of the Workflow Designer samples.
Workflow Image
There are four versions of the workflow available. The workflow with mapping for single-end reads looks as follows:
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<center> <br> <img src="/wiki/download/attachments/13008932/raw_rnaseq_single-end_with_tophat.png"/> <br> </center> |
The workflow with mapping for paired-end short appearance is the following:
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<center> <br> <img src="/wiki/download/attachments/13008932/raw_rnaseq_paired-end_with_tophat.png"/> <br> </center> |