Assembly using Tophat2 and annotation
Version 1

Stable

Alignment, assembly and annotation of generated transcripts from RNASEQ 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
bed_file bed_file runtime parameter for tool Filter SAM or BAM, output SAM or BAM 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
query query runtime parameter for tool NCBI BLAST+ blastp n/a
query query runtime parameter for tool NCBI BLAST+ blastp 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 Map with BWA-MEM toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1
10 MultiQC toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7
11 Filter SAM or BAM, output SAM or BAM toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.8+galaxy1
12 Illumina filtered reads toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1
13 TopHat toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/2.1.1
14 Cufflinks toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.2
15 Cuffmerge toolshed.g2.bx.psu.edu/repos/devteam/cuffmerge/cuffmerge/2.2.1.1
16 Cuffquant toolshed.g2.bx.psu.edu/repos/devteam/cuffquant/cuffquant/2.2.1.1
17 Cuffdiff toolshed.g2.bx.psu.edu/repos/devteam/cuffdiff/cuffdiff/2.2.1.5
18 gffread toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.2
19 TransDecoder toolshed.g2.bx.psu.edu/repos/iuc/transdecoder/transdecoder/3.0.1
20 Antismash toolshed.g2.bx.psu.edu/repos/bgruening/antismash/antismash/4.1
21 Glimmer ICM builder toolshed.g2.bx.psu.edu/repos/bgruening/glimmer3/glimmer_build-icm/0.2
22 NCBI BLAST+ makeblastdb toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.3.3
23 NCBI BLAST+ blastp toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/0.3.3
24 NCBI BLAST+ blastp toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/0.3.3
25 jackhmmer toolshed.g2.bx.psu.edu/repos/iuc/hmmer3/hmmer_jackhmmer/0.1.0
26 Glimmer3 toolshed.g2.bx.psu.edu/repos/bgruening/glimmer3/glimmer_knowlegde-based/0.2
27 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
bam_output bam_output n/a bam
stats stats n/a input
html_report html_report n/a html
output1 output1 n/a sam
forward forward n/a fasta
reverse reverse n/a fasta
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
out_file out_file n/a cxb
splicing_diff splicing_diff n/a tabular
promoters_diff promoters_diff n/a tabular
cds_diff cds_diff n/a tabular
cds_exp_fpkm_tracking cds_exp_fpkm_tracking n/a tabular
cds_fpkm_tracking cds_fpkm_tracking n/a tabular
tss_groups_exp tss_groups_exp n/a tabular
tss_groups_fpkm_tracking tss_groups_fpkm_tracking n/a tabular
genes_exp genes_exp n/a tabular
genes_fpkm_tracking genes_fpkm_tracking n/a tabular
isoforms_exp isoforms_exp n/a tabular
isoforms_fpkm_tracking isoforms_fpkm_tracking n/a tabular
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
outfile outfile n/a data
output1 output1 n/a tabular
output1 output1 n/a tabular
output output n/a txt
tblout tblout n/a txt
domtblout domtblout n/a txt
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: 344   Downloads: 22

Created: 18th Jun 2020 at 00:17

Last updated: 1st Jul 2020 at 09:55

Last used: 21st Oct 2020 at 08:42

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