Assembly using Tophat2 and annotation (alternate)
Version 1

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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Created: 18th Jun 2020 at 00:03

Last updated: 1st Jul 2020 at 10:03

Last used: 3rd Jul 2020 at 14:15

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