Prokaryotic Paired-End Analysis
Created: 2015-02-28 16:28:08
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Workflow Components
Inputs (17)
| Name |
Description |
| Upstream Read Files |
|
| Downstream Read Files |
|
| reference_genome |
runtime parameter for tool Align with Bowtie2 |
| library |
runtime parameter for tool Align with Bowtie2 |
| library |
runtime parameter for tool Align with Bowtie2 |
| library_type |
runtime parameter for tool Cufflinks Prokaryotic |
| min_isoform_fraction |
runtime parameter for tool Cufflinks Prokaryotic |
| max_bundle_frags |
runtime parameter for tool Cufflinks Prokaryotic |
| multiread_correct |
runtime parameter for tool Cufflinks Prokaryotic |
| pre_mrna_fraction |
runtime parameter for tool Cufflinks Prokaryotic |
| max_intron_len |
runtime parameter for tool Cufflinks Prokaryotic |
| overlap_radius |
runtime parameter for tool Cufflinks Prokaryotic |
| reference_annotation |
runtime parameter for tool Cufflinks Prokaryotic |
| reference_annotation |
runtime parameter for tool Cufflinks Prokaryotic |
| do_normalization |
runtime parameter for tool Cufflinks Prokaryotic |
| zero_regions |
runtime parameter for tool Create a BedGraph of genome coverage |
| strand |
runtime parameter for tool Create a BedGraph of genome coverage |
Steps (7)
| Name |
Tool |
Description |
| Input dataset |
None |
|
| Input dataset |
None |
|
| Align with Bowtie2 |
bowtie2 |
|
| BAM to BigWig |
bam_to_bigwig |
|
| Cufflinks Prokaryotic |
cufflinks_prok |
|
| BAM to BigWig |
bam_to_bigwig |
|
| Create a BedGraph of genome coverage |
bedtools_genomecoveragebed_bedgraph |
|
Outputs (10)
| Name |
Type |
| output_unaligned_reads_l |
fastqsanger |
| output_unaligned_reads_r |
fastqsanger |
| output |
bam |
| out |
bigwig |
| genes_expression |
tabular |
| transcripts_expression |
tabular |
| assembled_isoforms |
gtf |
| total_map_mass |
txt |
| out |
bigwig |
| output |
bedgraph |
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