Stable
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 |

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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

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