| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/0.9 |
| toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/0.7 (this tool) |
| toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/0.6 |
| tophat2 |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| samtools | 0.1.18 | package |
| bowtie2 | 2.1.0 | package |
| tophat2 | 2.0.9 | package |
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
refGenomeSource|genomeSource: indexed refGenomeSource|index: tophat_test singlePaired|sPaired: single params|settingsType: preSet singlePaired|input1: tophat_in2.fastqsanger |
junctions: tophat2_out1j.bed accepted_hits: tophat_out1h.bam |
tophat_in2.fastqsanger tophat2_out1j.bed tophat_out1h.bam |
| Test-2 |
params|settingsType: preSet singlePaired|mate_inner_distance: 20 singlePaired|sPaired: paired singlePaired|input2: tophat_in3.fastqsanger singlePaired|input1: tophat_in2.fastqsanger refGenomeSource|genomeSource: history refGenomeSource|ownFile: tophat_in1.fasta |
junctions: tophat2_out2j.bed accepted_hits: tophat_out2h.bam |
tophat_in2.fastqsanger tophat_in3.fastqsanger tophat_in1.fasta tophat2_out2j.bed tophat_out2h.bam |
| Test-3 |
params|settingsType: preSet singlePaired|mate_inner_distance: 20 singlePaired|sPaired: paired_collection singlePaired|input: paired collection refGenomeSource|genomeSource: history refGenomeSource|ownFile: tophat_in1.fasta |
junctions: tophat2_out2j.bed accepted_hits: tophat_out2h.bam |
tophat_in2.fastqsanger tophat_in3.fastqsanger tophat_in1.fasta tophat2_out2j.bed tophat_out2h.bam |
| Test-4 |
params|seg_mismatches: 2 params|settingsType: full params|fusion_search|anchor_len: 21 params|coverage_search|min_coverage_intron: 50 params|fusion_search|multireads: 4 params|own_junctions|raw_juncs|use_juncs: No params|coverage_search|use_search: Yes params|splice_mismatches: 0 singlePaired|sPaired: single params|indel_search|max_insertion_length: 3 singlePaired|input1: tophat_in2.fastqsanger params|indel_search|allow_indel_search: Yes params|seg_length: 25 params|min_intron_length: 70 params|library_type: fr-unstranded params|min_segment_intron: 50 params|fusion_search|ignore_chromosomes: chrM params|fusion_search|min_dist: 10000021 params|max_intron_length: 500000 params|own_junctions|use_junctions: Yes params|bowtie_n: No params|read_mismatches: 2 params|max_multihits: 40 params|fusion_search|multipairs: 5 params|fusion_search|do_search: Yes params|anchor_length: 8 params|max_segment_intron: 500000 params|microexon_search: Yes params|bowtie2_settings|b2_settings: No params|fusion_search|read_mismatches: 3 params|own_junctions|gene_model_ann|use_annotations: No refGenomeSource|genomeSource: history refGenomeSource|ownFile: tophat_in1.fasta params|coverage_search|max_coverage_intron: 20000 params|indel_search|max_deletion_length: 3 |
insertions: tophat_out3i.bed deletions: tophat_out3d.bed junctions: tophat2_out3j.bed accepted_hits: tophat_out3h.bam |
tophat_in2.fastqsanger tophat_in1.fasta tophat_out3i.bed tophat_out3d.bed tophat2_out3j.bed tophat_out3h.bam |
| Test-5 |
params|seg_mismatches: 2 params|settingsType: full singlePaired|report_discordant_pairs: Yes params|bowtie2_settings|b2_settings: No params|fusion_search|multipairs: 5 params|fusion_search|multireads: 4 params|own_junctions|raw_juncs|use_juncs: No params|coverage_search|use_search: No params|splice_mismatches: 0 params|read_edit_dist: 5 singlePaired|input2: tophat_in3.fastqsanger singlePaired|input1: tophat_in2.fastqsanger params|indel_search|allow_indel_search: No params|seg_length: 25 singlePaired|sPaired: paired params|min_intron_length: 70 params|library_type: fr-unstranded params|min_segment_intron: 50 params|fusion_search|ignore_chromosomes: chrM params|fusion_search|min_dist: 10000021 singlePaired|mate_inner_distance: 20 params|max_intron_length: 500000 params|own_junctions|use_junctions: Yes params|bowtie_n: Yes params|read_mismatches: 5 params|max_multihits: 40 params|microexon_search: Yes params|fusion_search|do_search: Yes params|anchor_length: 8 params|max_segment_intron: 500000 refGenomeSource|index: tophat_test params|fusion_search|anchor_len: 21 params|fusion_search|read_mismatches: 3 params|own_junctions|gene_model_ann|use_annotations: No refGenomeSource|genomeSource: indexed |
junctions: tophat2_out4j.bed accepted_hits: tophat_out4h.bam |
tophat_in2.fastqsanger tophat_in3.fastqsanger tophat2_out4j.bed tophat_out4h.bam |