TopHat2-SE
TopHat 2.0.9 (for single-end reads) is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the short read aligner Bowtie and analyzes the mapping results to identify splice junctions between exons. Earlier versions of TopHat are also supported.
App Creator
Sheldon Mckay
Test Data
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Test data for this app appears directly in the Discovery Environment in the Data window under _Community Data -> iplantcollaborative -> example_data -> tophat2-SE |
Input File(s)
- Select one or more of the example files as input files for tophat2-SE
- Select the Arabidopsis thaliana reference genome and annotations from the pull-down menu
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 next section below.
Name | Type | Value |
|---|---|---|
Align read files | Selection | in serial |
FASTQ file(s) | Input | /iplant/home/shared/iplantcollaborative/example_data/tophat2-SE/SRR070570_WT_rep1.fastq |
FASTQ file(s) | Input | /iplant/home/shared/iplantcollaborative/example_data/tophat2-SE/SRR070571_WT_rep2.fastq |
FASTQ file(s) | Input | /iplant/home/shared/iplantcollaborative/example_data/tophat2-SE/SRR070572_hy5_rep1.fastq |
FASTQ file(s) | Input | /iplant/home/shared/iplantcollaborative/example_data/tophat2-SE/SRR070573_hy5_rep2.fastq |
Select a reference genome from the list | Input | Arabidopsis thaliana (Ensembl 14) |
Provide a reference genome file in FASTA format | Input | |
Select Reference Annotations | Input | Arabidopsis thaliana (Ensembl 14) |
Provide a reference annotation file (GTF) | Input | |
FASTQ Quality Scale | Selection | Sanger (PHRED33) |
Library Type | Text | fr-unstranded |
Anchor length | Number | 8 |
Maximum number of mismatches that can appear in the anchor region of spliced alignment | Number | 0 |
The minimum intron length | Number | 70 |
The maximum intron length | Number | 50000 |
Minimum isoform fraction | Number | 0.15 |
Maximum number of alignments to be allowed | Number | 20 |
Minimum intron length that may be found during split-segment (default) search. | Number | 50 |
Maximum intron length that may be found during split-segment (default) search | Number | 500000 |
Number of mismatches allowed in each segment alignment for reads mapped independently | Number | 2 |
Minimum length of read segments | Number | 20 |
Do not convert output to BAM format | Flag | false |
Number of threads | Number | 6 |
Bowtie 2 speed and sensitivity | Selection | Sensitive (slower) |
Tophat Version | Selection | 2.0.9 |
Bowtie Version | Selection | 2.1.0 |
Output File(s)
- Expect a the following files as output
- The output folder will be named tophat_out if all reads are mapped together in one pass.
- If multiple read files are mapped in serial (one file at a time) the output for each set will be in a folder named after the input file and all bam files will be copied to the bam folder
| No Format |
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??? logs
??? [truncated for readiability]
??? tophat_out
??? accepted_hits.bam
??? align_summary.txt
??? deletions.bed
??? insertions.bed
??? junctions.bed
??? logs
??? [truncated for readiability]
??? prep_reads.info
??? unmapped.bam
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Related Tutorials
More information
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This app has been deprecated and is no longer available. Please use a Hisat2 app in the DE, which more efficiently and accurately provides the same core functionality (i.e., spliced alignment of RNA-Seq reads). If you cannot find a suitable replacement, please contact CyVerse Support at support@cyverse.org. |