Assembly using Tophat2 and annotation (alternate) Version 1
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Alignment, assembly and annotation of RNQSEQ reads using TOPHAT (without filtering out host reads).
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| mask_data_file | mask_data_file | runtime parameter for tool NCBI BLAST+ makeblastdb | n/a |
| mask_data_file | mask_data_file | runtime parameter for tool NCBI BLAST+ makeblastdb | n/a |
| chr_replace | chr_replace | runtime parameter for tool gffread | n/a |
| mask_data_file | mask_data_file | runtime parameter for tool NCBI BLAST+ makeblastdb | n/a |
Steps
| ID | Name | Description |
|---|---|---|
| 0 | List of Illumina accessions | |
| 1 | Reference genome. | |
| 2 | Reference annotation | |
| 3 | UniProt | toolshed.g2.bx.psu.edu/repos/galaxyp/uniprotxml_downloader/uniprotxml_downloader/2.1.0 |
| 4 | SARS-CoV-2 proteins | |
| 5 | Illumina data | toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.4 |
| 6 | NCBI BLAST+ makeblastdb | toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.3.3 |
| 7 | NCBI BLAST+ makeblastdb | toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.3.3 |
| 8 | fastp: Trimmed Illumina Reads | toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.19.5+galaxy1 |
| 9 | MultiQC | toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7 |
| 10 | TopHat | toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/2.1.1 |
| 11 | Cufflinks | toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.2 |
| 12 | Cuffmerge | toolshed.g2.bx.psu.edu/repos/devteam/cuffmerge/cuffmerge/2.2.1.1 |
| 13 | gffread | toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.2 |
| 14 | TransDecoder | toolshed.g2.bx.psu.edu/repos/iuc/transdecoder/transdecoder/3.0.1 |
| 15 | Antismash | toolshed.g2.bx.psu.edu/repos/bgruening/antismash/antismash/4.1 |
| 16 | Glimmer ICM builder | toolshed.g2.bx.psu.edu/repos/bgruening/glimmer3/glimmer_build-icm/0.2 |
| 17 | jackhmmer | toolshed.g2.bx.psu.edu/repos/iuc/hmmer3/hmmer_jackhmmer/0.1.0 |
| 18 | NCBI BLAST+ makeblastdb | toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.3.3 |
| 19 | NCBI BLAST+ blastp | toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/0.3.3 |
| 20 | NCBI BLAST+ blastp | toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/0.3.3 |
| 21 | Glimmer3 | toolshed.g2.bx.psu.edu/repos/bgruening/glimmer3/glimmer_knowlegde-based/0.2 |
| 22 | NCBI BLAST+ blastp | toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/0.3.3 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| proteome | proteome | n/a | uniprotxml |
| list_paired | list_paired | n/a | input |
| output_collection | output_collection | n/a | input |
| output_collection_other | output_collection_other | n/a | input |
| log | log | n/a | txt |
| outfile | outfile | n/a | data |
| outfile | outfile | n/a | data |
| output_paired_coll | output_paired_coll | n/a | input |
| report_html | report_html | n/a | html |
| report_json | report_json | n/a | json |
| stats | stats | n/a | input |
| html_report | html_report | n/a | html |
| align_summary | align_summary | n/a | txt |
| insertions | insertions | n/a | bed |
| deletions | deletions | n/a | bed |
| junctions | junctions | n/a | bed |
| accepted_hits | accepted_hits | n/a | bam |
| genes_expression | genes_expression | n/a | tabular |
| transcripts_expression | transcripts_expression | n/a | tabular |
| assembled_isoforms | assembled_isoforms | n/a | gtf |
| total_map_mass | total_map_mass | n/a | txt |
| skipped | skipped | n/a | gtf |
| merged_transcripts | merged_transcripts | n/a | gtf |
| output_exons | output_exons | n/a | fasta |
| transdecoder_pep | transdecoder_pep | n/a | fasta |
| transdecoder_cds | transdecoder_cds | n/a | fasta |
| transdecoder_bed | transdecoder_bed | n/a | bed |
| transdecoder_gff3 | transdecoder_gff3 | n/a | gff3 |
| genecluster_tabular | genecluster_tabular | n/a | input |
| genbank | genbank | n/a | input |
| embl | embl | n/a | input |
| archive | archive | n/a | input |
| html | html | n/a | html |
| outfile | outfile | n/a | data |
| output | output | n/a | txt |
| tblout | tblout | n/a | txt |
| domtblout | domtblout | n/a | txt |
| outfile | outfile | n/a | data |
| output1 | output1 | n/a | tabular |
| output1 | output1 | n/a | tabular |
| genes_output | genes_output | n/a | fasta |
| report_output | report_output | n/a | txt |
| detailed_output | detailed_output | n/a | txt |
| output1 | output1 | n/a | tabular |
Creators and Submitter
License
Activity
Views: 429 Downloads: 36
Created: 18th Jun 2020 at 00:03
Last updated: 1st Jul 2020 at 10:03
Last used: 17th Jan 2021 at 02:03
AttributionsNone
Related items
Ongoing analysis of COVID-19 using Galaxy, BioConda and public research infrastructures https://covid19.galaxyproject.org
Space: COVID-19 Biohackathon
Public web page: https://github.com/galaxyproject/SARS-CoV-2
