COVID-19: assembly using Tophat2 and annotation (alternate)


StepAnnotation
Step 1: Input dataset
select at runtime
Step 2: Input dataset
select at runtime
Step 3: Input dataset
select at runtime
Step 4: UniProt
A Common Organism
9606
Nothing selected.
fasta
Step 5: Input dataset
select at runtime
Step 6: Faster Download and Extract Reads in FASTQ
List of SRA accession, one per line
Output dataset 'output' from step 1
Advanced Options:
Not available.
--split-3: write properly paired biological reads into different files and single reads in another file
True
Step 7: NCBI BLAST+ makeblastdb
protein
Output dataset 'proteome' from step 4
Empty.
False
True
select at runtime
Do not assign a Taxonomy ID to the sequences
Step 8: NCBI BLAST+ makeblastdb
protein
Output dataset 'output' from step 5
Empty.
False
True
select at runtime
Do not assign a Taxonomy ID to the sequences
Step 9: fastp
Paired Collection
Output dataset 'list_paired' from step 6
Adapter Trimming Options:
False
Empty.
Empty.
Global trimming options:
Not available.
Not available.
Not available.
Not available.
Overrepresented Sequence Analysis:
False
Not available.
Filter Options:
Quality filtering options:
False
20
20
Not available.
Length filtering options:
False
50
Low complexity filtering options:
False
Not available.
Read Modification Options:
Automatic trimming for Illumina NextSeq/NovaSeq data
Not available.
Disable polyX trimming
UMI processing:
False
Empty.
Not available.
Empty.
Per read cutting by quality options:
False
False
Not available.
Not available.
Base correction by overlap analysis options:
False
Output Options:
True
True
Step 10: MultiQC
Results
Results 1
fastp
Output dataset 'report_json' from step 9
Empty.
Empty.
False
Step 11: TopHat
Paired-end (as collection)
Output dataset 'output_paired_coll' from step 9
300
20
Yes
Use a genome from history
Output dataset 'output' from step 2
Use Defaults
No
Step 12: Cufflinks
Output dataset 'accepted_hits' from step 11
300000
0.1
0.15
No
No
No
Cufflinks Effective Length Correction
select at runtime
No
Step 13: Cuffmerge
Output dataset 'skipped' from step 12
Additional GTF Inputs (Lists)s
Yes
Output dataset 'output' from step 3
No
0.05
Step 14: gffread
Output dataset 'merged_transcripts' from step 13
Nothing selected.
No
Not available.
select at runtime
none
From your history
Output dataset 'output' from step 2
Nothing selected.
fasta file with spliced exons for each GFF transcript (-w exons.fa) for each fasta: record the exon coordinates projected onto the spliced sequence (-W)
none
False
False
False
Step 15: TransDecoder
Output dataset 'output_exons' from step 14
100
Advanced Options:
False
universal
Not available.
900
False
Training Options:
Train with the top longest ORFs
500
Step 16: Antismash
Output dataset 'output_exons' from step 14
Bacteria
Nucleotide
False
True
True
True
True
True
True
False
True
HTML file All results EMBL files GenBank files Gene clusters
Step 17: Unknown Tool with id 'toolshed.g2.bx.psu.edu/repos/bgruening/glimmer3/glimmer_build-icm/0.2'
Step 18: jackhmmer
Output dataset 'transdecoder_cds' from step 15
5
Output dataset 'proteome' from step 4
Table of per-sequence hits (--tblout) Table of per-domain hits (--domtblout)
False
False
False
Disable
10.0
10.0
Not available.
Not available.
Not available.
Not available.
Not available.
Not available.
False
0.02
0.001
1e-05
False
Assign columns with >= symfrac residues as consensus (--fast)
0.5
0.5
Henikoff position-based weights (--wpb)
Disabled
Unspecified
200
200
200
200
100
200
0.04
False
Not available.
Not available.
42
Step 19: NCBI BLAST+ makeblastdb
protein
Output dataset 'transdecoder_pep' from step 15
Empty.
False
True
select at runtime
Do not assign a Taxonomy ID to the sequences
Step 20: NCBI BLAST+ blastp
Output dataset 'transdecoder_pep' from step 15
BLAST database from your history
Empty.
Output dataset 'outfile' from step 7
Empty.
blastp - Traditional BLASTP to compare a protein query to a protein database
0.001
Tabular (extended 25 columns)
Hide Advanced Options
Step 21: NCBI BLAST+ blastp
Output dataset 'transdecoder_pep' from step 15
BLAST database from your history
Empty.
Output dataset 'outfile' from step 8
Empty.
blastp - Traditional BLASTP to compare a protein query to a protein database
0.001
Tabular (extended 25 columns)
Hide Advanced Options
Step 22: Unknown Tool with id 'toolshed.g2.bx.psu.edu/repos/bgruening/glimmer3/glimmer_knowlegde-based/0.2'
Step 23: NCBI BLAST+ blastp
Output dataset 'proteome' from step 4
BLAST database from your history
Empty.
Output dataset 'outfile' from step 19
Empty.
blastp - Traditional BLASTP to compare a protein query to a protein database
0.001
Tabular (extended 25 columns)
Hide Advanced Options