StringTie assembly and annotation
Version 1

Stable

Alignment, assembly and annotation of RNASEQ reads as well as annotation of generated transcripts.

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

Steps

ID Name Description
0 List of Illumina accessions
1 Reference genome
2 Reference genome 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 Map with BWA-MEM toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1
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 HISAT2 toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy5
14 StringTie toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.1.1
15 StringTie merge toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/2.1.1
16 gffread toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.2
17 Glimmer ICM builder toolshed.g2.bx.psu.edu/repos/bgruening/glimmer3/glimmer_build-icm/0.2
18 Antismash toolshed.g2.bx.psu.edu/repos/bgruening/antismash/antismash/4.1
19 TransDecoder toolshed.g2.bx.psu.edu/repos/iuc/transdecoder/transdecoder/3.0.1
20 Glimmer3 toolshed.g2.bx.psu.edu/repos/bgruening/glimmer3/glimmer_knowlegde-based/0.2
21 jackhmmer toolshed.g2.bx.psu.edu/repos/iuc/hmmer3/hmmer_jackhmmer/0.1.0
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 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
bam_output bam_output n/a bam
output1 output1 n/a sam
forward forward n/a fasta
reverse reverse n/a fasta
output_alignments output_alignments n/a bam
output_gtf output_gtf n/a gtf
coverage coverage n/a gtf
gene_counts gene_counts n/a tabular
transcript_counts transcript_counts n/a tabular
out_gtf out_gtf n/a gtf
output_exons output_exons n/a fasta
outfile outfile n/a data
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
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
genes_output genes_output n/a fasta
report_output report_output n/a txt
detailed_output detailed_output n/a txt
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
output1 output1 n/a tabular
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Created: 18th Jun 2020 at 00:13

Last updated: 1st Jul 2020 at 09:57

Last used: 4th Jul 2020 at 22:21

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