Assembly using Tophat2 and annotation (alternate)
Version 1

Workflow Type: Galaxy

Alignment, assembly and annotation of RNQSEQ reads using TOPHAT (without filtering out host reads).


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


ID Name Description
0 List of Illumina accessions
1 Reference genome.
2 Reference annotation
3 UniProt
4 SARS-CoV-2 proteins
5 Illumina data
6 NCBI BLAST+ makeblastdb
7 NCBI BLAST+ makeblastdb
8 fastp: Trimmed Illumina Reads
9 MultiQC
10 TopHat
11 Cufflinks
12 Cuffmerge
13 gffread
14 TransDecoder
15 Antismash
16 Glimmer ICM builder
17 jackhmmer
18 NCBI BLAST+ makeblastdb
19 NCBI BLAST+ blastp
20 NCBI BLAST+ blastp
21 Glimmer3
22 NCBI BLAST+ blastp


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
help Creators and Submitter
Not specified

Views: 930   Downloads: 63

Created: 18th Jun 2020 at 00:03

Last updated: 1st Jul 2020 at 10:03

Last used: 6th Dec 2021 at 14:49

help Attributions


Version History

Version 1 Created 18th Jun 2020 at 00:03 by Ambarish Kumar

No revision comments

Related items

Powered by
Copyright © 2008 - 2021 The University of Manchester and HITS gGmbH