RNA-Seq analysis from fastq

Created: 2020-03-18 09:16:12 Last updated: 2020-03-18 09:16:57

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Inputs (39)

Name	Description
inputFile	runtime parameter for tool Collect Alignment Summary Metrics
input	runtime parameter for tool Flatten Collection
input	runtime parameter for tool Filter List
how	runtime parameter for tool Filter List
input	runtime parameter for tool Select
input	runtime parameter for tool Flatten Collection
input	runtime parameter for tool Flatten Collection
input	runtime parameter for tool Flatten Collection
input	runtime parameter for tool Add input name as column
batch_factors	runtime parameter for tool DESeq2
input	runtime parameter for tool Cut
input	runtime parameter for tool Cut
datasets	runtime parameter for tool Export datasets to cluster
datasets	runtime parameter for tool Export datasets to cluster
datasets	runtime parameter for tool Export datasets to cluster
datasets	runtime parameter for tool Export datasets to cluster
inputs	runtime parameter for tool Concatenate datasets
input	runtime parameter for tool Flatten Collection
input	runtime parameter for tool Select first
contaminants	runtime parameter for tool FastQC
limits	runtime parameter for tool FastQC
input_file	runtime parameter for tool FastQC
input	runtime parameter for tool Filter List
how	runtime parameter for tool Filter List
input_collection	runtime parameter for tool Extract Element
input	runtime parameter for tool Select
input	runtime parameter for tool Add input name as column
input	runtime parameter for tool Cut
inputs	runtime parameter for tool Concatenate datasets
datasets	runtime parameter for tool Export datasets to cluster
readtype	runtime parameter for tool Trimmomatic
contaminants	runtime parameter for tool FastQC
limits	runtime parameter for tool FastQC
input_file	runtime parameter for tool FastQC
library	runtime parameter for tool Bowtie2
infile	runtime parameter for tool Replace
input	runtime parameter for tool Flatten Collection
samfile	runtime parameter for tool htseq-count
gfffile	runtime parameter for tool htseq-count

Steps (37)

Name	Tool	Description
Input dataset collection	None
Input dataset	None
Collect Alignment Summary Metrics	toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CASM/2.18.2.1
Merge Collections	__MERGE_COLLECTION__
Flatten Collection	__FLATTEN__
Filter List	__FILTER_FROM_FILE__
Select	Grep1
Flatten Collection	__FLATTEN__
Flatten Collection	__FLATTEN__
Flatten Collection	__FLATTEN__
Add input name as column	toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.1.1
MultiQC	toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.6
Input dataset	None
DESeq2	toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.2
Cut	Cut1
Cut	Cut1
Export datasets to cluster	toolshed.g2.bx.psu.edu/repos/earlhaminst/export_to_cluster/export_to_cluster/0.0.2
Export datasets to cluster	toolshed.g2.bx.psu.edu/repos/earlhaminst/export_to_cluster/export_to_cluster/0.0.2
Export datasets to cluster	toolshed.g2.bx.psu.edu/repos/earlhaminst/export_to_cluster/export_to_cluster/0.0.2
Export datasets to cluster	toolshed.g2.bx.psu.edu/repos/earlhaminst/export_to_cluster/export_to_cluster/0.0.2
Concatenate datasets	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0
Flatten Collection	__FLATTEN__
Select first	Show beginning1
FastQC	toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72
Filter List	__FILTER_FROM_FILE__
Extract Element	toolshed.g2.bx.psu.edu/repos/erasmus-medical-center/extract_element_from_collection/extract_element_from_collection/0.1
Select	Grep1
Add input name as column	toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.1.1
Cut	Cut1
Concatenate datasets	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0
Export datasets to cluster	toolshed.g2.bx.psu.edu/repos/earlhaminst/export_to_cluster/export_to_cluster/0.0.2
Trimmomatic	toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.36.5
FastQC	toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72
Bowtie2	toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.3+galaxy0
Replace	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.1
Flatten Collection	__FLATTEN__
htseq-count	toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.9.1

Outputs (57)

Name	Type
outFile	tabular
output	input
output	input
output_filtered	input
output_discarded	input
out_file1	input
output	input
output	input
output	input
output	tabular
stats	input
html_report	html
log	txt
split_output	input
deseq_out	tabular
plots	pdf
counts_out	tabular
out_file1	tabular
out_file1	tabular
log	txt
log	txt
log	txt
log	txt
out_file1	input
output	input
out_file1	input
html_file	html
text_file	txt
output_filtered	input
output_discarded	input
output	auto
extracted	auto
out_file1	input
output	tabular
out_file1	tabular
out_file1	input
log	txt
fastq_out_paired	input
fastq_out_unpaired	input
fastq_out_r1_paired	input
fastq_out_r2_paired	input
fastq_out_r1_unpaired	input
fastq_out_r2_unpaired	input
fastq_out	input
html_file	html
text_file	txt
output_unaligned_reads_l	fastqsanger
output_aligned_reads_l	fastqsanger
output_aligned_reads_r	fastqsanger
output_unaligned_reads_r	fastqsanger
output	bam
mapping_stats	txt
outfile	input
output	input
counts	tabular
othercounts	tabular
samoutfile	bam

Information Workflow Type

Galaxy

Information Uploader

Miriam Payá

Information License

All versions of this Workflow are licensed under:

Information Version 1 (of 1)

Information Credits (1)

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Miriam Payá

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Information Statistics

906 viewings

650 downloads

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RNA-Seq analysis from fastq

Created by Miriam Payá on Wednesday 18 March 2020 09:16:11 (UTC)

Last edited by Miriam Payá on Wednesday 18 March 2020 09:16:57 (UTC)

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