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Cufflinks 2.2.1
This App runs Cufflinks (version 2+) to assemble transcripts using Sequence alignments (BAM) generated by TopHat/Bowtie.
App Creator
Upendra Devisetty
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Quick Start
- Cufflinks 2.2.1
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Quick Start
- Cufflinks 2.0 requires a text file of SAM alignments or a binary SAM (BAM) file as input. For more details, see the specification. It is recommended that you use reads generated by TopHat as input files.
Test Data
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Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplant_training -> intro_rna-seq -> 02_tophat |
Input File(s)
Use the accepted_hits.bam files from the hy5 and WT rep1 and rep2 directories for an example run. Notes below are directly from Cufflinks user manual.
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sort -k 3,3 -k 4,4n hits.sam > hits.sam.sorted
Parameters Used in App
When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the section below.
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Leave all other parameters as default.
Output File(s)
Cufflinks produces 3 main output files (notes directly from Cufflinks user manual):
1) transcripts.gtf
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In the directory Community Data -> iplant_training -> intro_rna-seq -> 03_cufflinks, you will see directories for each of the selected bam files used as inputs. These directories also contain a "skipped.gtf" file.
Related Tutorials
Tool Source for App
- https://github.com/cole-trapnell-lab/cufflinks
- Customized script to call the Cufflinks binary has been drafted by Sheldon McKay, thus not all advanced options available are exposed.