{"type":"doc","content":[{"type":"heading","attrs":{"level":3},"content":[{"text":"RSEM-Prepare-Reference-1.2.19","type":"text"}]},{"type":"blockquote","content":[{"type":"paragraph","content":[{"text":"Description and Quick Start","type":"text","marks":[{"type":"strong"},{"type":"textColor","attrs":{"color":"#000000"}}]}]},{"type":"extension","attrs":{"extensionType":"com.atlassian.confluence.migration","extensionKey":"legacy-content","text":"","parameters":{"cxhtml":"

Prepares transcripts from genome files and matching GTF files.
Test Data:
Community Data > iplantcollaborative > example_data > RSEM_prepare_reference > input
Input Files -- 2 files needed. A genome sequence file, and a matching .gtf annotation or assembly file. The test files are genome.fas and annotation.gtf

","nestedContent":{"type":"doc","content":[{"type":"blockquote","content":[{"type":"paragraph","content":[{"text":"Prepares transcripts from genome files and matching GTF files. ","type":"text","marks":[{"type":"textColor","attrs":{"color":"#000000"}}]}]},{"type":"blockquote","content":[{"type":"paragraph","content":[{"text":"Test Data:","type":"text","marks":[{"type":"textColor","attrs":{"color":"#000000"}}]}]}]},{"type":"blockquote","content":[{"type":"paragraph","content":[{"text":" ","type":"text","marks":[{"type":"textColor","attrs":{"color":"#000000"}}]},{"text":"Community Data > iplantcollaborative > example_data > RSEM_prepare_reference > input","type":"text","marks":[{"type":"textColor","attrs":{"color":"#000000"}}]}]}]},{"type":"blockquote","content":[{"type":"paragraph","content":[{"text":" ","type":"text","marks":[{"type":"textColor","attrs":{"color":"#000000"}}]},{"text":"Input Files -- ","type":"text","marks":[{"type":"textColor","attrs":{"color":"#000000"}}]},{"text":"2 files needed. A genome sequence file, and a matching .gtf annotation or assembly file. The test files are genome.fas and annotation.gtf","type":"text","marks":[{"type":"textColor","attrs":{"color":"#000000"}}]}]}]}]}],"version":1}}}}]},{"type":"paragraph","content":[{"text":"Parameters Used in App: ","type":"text","marks":[{"type":"textColor","attrs":{"color":"#000000"}}]},{"text":"No special parameters or options. ","type":"text","marks":[{"type":"textColor","attrs":{"color":"#000000"}}]}]},{"type":"paragraph","content":[{"text":"Output Files: ","type":"text","marks":[{"type":"textColor","attrs":{"color":"#000000"}}]},{"text":"A series of files is created. The main one of interest is the transcript sequence file. Others list the chromosomes or scaffolds in an assembly, and other intermediate files.","type":"text","marks":[{"type":"textColor","attrs":{"color":"#000000"}}]}]},{"type":"paragraph","content":[{"text":"Test output files: ","type":"text","marks":[{"type":"textColor","attrs":{"color":"#000000"}}]},{"text":"Community Data > iplantcollaborative > example_data > output > RSEM_prepare_reference","type":"text","marks":[{"type":"textColor","attrs":{"color":"#000000"}}]},{"text":"> ","type":"text","marks":[{"type":"textColor","attrs":{"color":"#000000"}}]},{"text":"Arabidopsis.transcripts.fa","type":"text"}]},{"type":"heading","attrs":{"level":4},"content":[{"text":"References","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"https://biowize.wordpress.com/2014/03/04/understanding-rsem-raw-read-counts-vs-expected-counts/","type":"text","marks":[{"type":"link","attrs":{"href":"https://biowize.wordpress.com/2014/03/04/understanding-rsem-raw-read-counts-vs-expected-counts/"}}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"http://trinityrnaseq.sourceforge.net/analysis/abundance_estimation.html","type":"text","marks":[{"type":"link","attrs":{"href":"http://trinityrnaseq.sourceforge.net/analysis/abundance_estimation.html"}}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"http://deweylab.biostat.wisc.edu/rsem/README.html","type":"text","marks":[{"type":"link","attrs":{"href":"http://deweylab.biostat.wisc.edu/rsem/README.html"}}]}]}]}]},{"type":"extension","attrs":{"extensionType":"com.atlassian.confluence.migration","extensionKey":"__confluenceADFMigrationUnsupportedContentInternalExtension__","text":"","parameters":{"cxhtml":"","unconsumed-attrs":true}}}],"version":1}

RSEM-Prepare-Reference 1.2.19

RSEM-Prepare-Reference-1.2.19

References