Detrprok

Created: 2013-05-20 22:29:45 Last updated: 2015-11-03 11:12:12

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In the case study of stranded and prokaryotic RNAseq data, the Det'Rprok workflow detects candidates of 3 kinds of non coding RNA: 5'UTRs, antisense RNAs, and small RNAs.

Inputs: i) an mapping file (bam format) containing one valid alignment by read, ii) a feature file (gff format) annotating the genomic sequences used for the mapping.

Dependencies (from the Galaxy toolshed): "s_mart", "detrprok_scripts"

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Import

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You may use Bowtie or another mapper (use appropriate mapping option to retain only uniquely mapping reads).","name":"read alignments on genome"}],"label":null,"name":"Input dataset","outputs":[],"position":{"left":200,"top":403},"tool_errors":null,"tool_id":null,"tool_state":"{\"name\": \"read alignments on genome\"}","tool_version":null,"type":"data_input","user_outputs":[],"uuid":"00d8d4c6-aca2-4eed-8844-cfa3cf9aa12c"},"2":{"annotation":"Select here the GFF file features that will be considered as initial annotations. Any term added here will cause pre-existing features with this term not to be predicted again by the workflow. Please use a comma separated list and use \"CDS\" rather than \"gene\" for protein coding genes. 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Workflow Components

Inputs (16)

Name	Description
genome annotations	Select here the GFF annotation file containing coding genes, tRNAs, rRNAs and known ncRNAs. You can download it from GJI (http://genome.jgi.doe.gov) or NCBI (http://ftp.ncbi.nih.gov/genomes/Bacteria). Caution: 1srt column should have exactly the same identifier as the genome sequence used for mapping.
read alignments on genome	Select here the bam file resulting from the mapping of RNA-seq reads on the genome sequence. You may use Bowtie or another mapper (use appropriate mapping option to retain only uniquely mapping reads).
distance	runtime parameter for tool clusterize
OptionMin	runtime parameter for tool restrict from size
OptionMin	runtime parameter for tool restrict from size
optionType	runtime parameter for tool clean transcript file
OptionMin	runtime parameter for tool select by tag
OptionMin	runtime parameter for tool select by tag
distance	runtime parameter for tool clusterize
distance	runtime parameter for tool clusterize
OptionMin	runtime parameter for tool restrict from size
OptionMin	runtime parameter for tool select by tag
distance	runtime parameter for tool clusterize
distance	runtime parameter for tool clusterize
OptionDistance	runtime parameter for tool compare overlapping small query
OptionDistance	runtime parameter for tool compare overlapping small query

Steps (43)

Name	Tool	Description
Input dataset	None
Input dataset	None
Concatenate datasets	cat1
clusterize	MergingDataClusterize
remove introns	removeIntrons
collapse reads	collapseReads
compare overlapping small query	CompareOverlappingSmallQuery
compare overlapping small query	CompareOverlappingSmallQuery
splitTranscriptGff	toolshed.g2.bx.psu.edu/repos/clairetn/detrprok_scripts/splitTranscriptGff/1.0.0
restrict from size	restrictFromSize
restrict from size	restrictFromSize
compare overlapping small reference	CompareOverlappingSmallRef
clean transcript file	CleanTranscriptFile
select by tag	SelectByTag
select by tag	SelectByTag
change tag name	changeTagName
clusterize	MergingDataClusterize
clusterize	MergingDataClusterize
Filter	Filter1
Filter	Filter1
Filter	Filter1
remove introns	removeIntrons
remove introns	removeIntrons
collapse reads	collapseReads
change GFF features	changeGffFeatures
change GFF features	changeGffFeatures
change GFF features	changeGffFeatures
change tag name	changeTagName
change tag name	changeTagName
restrict from size	restrictFromSize
change GFF features	changeGffFeatures
change GFF features	changeGffFeatures
select by tag	SelectByTag
colorGff	toolshed.g2.bx.psu.edu/repos/clairetn/detrprok_scripts/colorGff/1.0.0
clusterize	MergingDataClusterize
colorGff	toolshed.g2.bx.psu.edu/repos/clairetn/detrprok_scripts/colorGff/1.0.0
change GFF features	changeGffFeatures
colorGff	toolshed.g2.bx.psu.edu/repos/clairetn/detrprok_scripts/colorGff/1.0.0
clusterize	MergingDataClusterize
remove introns	removeIntrons
remove introns	removeIntrons
compare overlapping small query	CompareOverlappingSmallQuery
compare overlapping small query	CompareOverlappingSmallQuery

Outputs (41)

Name	Type
out_file1	input
outputFileGff	gff3
outputFile	gff3
outputFileGff	gff3
outputFileGff	gff3
outputFileGff	gff3
outputFile	gff3
outputFileGff	gff3
outputFileGff	gff3
outputFileGff	gff3
outputFile	gtf
outputFileGff	gff3
outputFileGff	gff3
outputFileGff	gff3
outputFileGff	gff3
outputFileGff	gff3
out_file1	input
out_file1	input
out_file1	input
outputFile	gff3
outputFile	gff3
outputFileGff	gff3
outputFile	gff
outputFile	gff
outputFile	gff
outputFileGff	gff3
outputFileGff	gff3
outputFileGff	gff3
outputFile	gff
outputFile	gff
outputFileGff	gff3
outputFile	gff
outputFileGff	gff3
outputFile	gff
outputFile	gff
outputFile	gff
outputFileGff	gff3
outputFile	gff3
outputFile	gff3
outputFileGff	gff3
outputFileGff	gff3

Information Workflow Type

Galaxy

Information Uploader

Clairetn

Information License

All versions of this Workflow are licensed under:

Information Version 4 (latest) (of 4)

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Information Statistics

4095 viewings

1314 downloads

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Citations (0)

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Version History

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Detrprok_wf

Created by Clairetn on Monday 20 May 2013 22:29:44 (UTC)

Last edited by Clairetn on Monday 20 May 2013 22:34:04 (UTC)
Detrprok_wf

Created by Clairetn on Monday 19 October 2015 12:59:34 (UTC)

Last edited by Clairetn on Thursday 22 October 2015 09:34:41 (UTC)
Detrprok_wf

Created by Clairetn on Thursday 22 October 2015 09:42:54 (UTC)

Last edited by Clairetn on Thursday 22 October 2015 09:49:27 (UTC)

Revision comment:

in order to follow the Galaxy releases
Detrprok

Created by Clairetn on Monday 02 November 2015 15:41:23 (UTC)

Last edited by Clairetn on Tuesday 03 November 2015 11:12:11 (UTC)

Revision comment:

2 error corrections: i) use transcription units in place of operon-like as inputs for the division between sRNA and asRNA ; ii) use a strict intergenic position for sRNA)

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