RNA-Seq analysis from fastq
Created: 2020-03-18 09:16:12
Last updated: 2020-03-18 09:16:57
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Workflow Components
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 | |
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 |
Workflow Type
Version 1
(of 1)
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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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