Detrprok

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

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Detect candidates of 3 kinds of ncRNA: long utr5', antisense and small RNA.
Use tools from Galaxy toolshed: "s_mart" and "detrprok_scripts"

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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).
OptionDistance	runtime parameter for tool compare overlapping small query
OptionMin	runtime parameter for tool restrict from size
OptionMin	runtime parameter for tool restrict from size
distance	runtime parameter for tool clusterize
OptionMin	runtime parameter for tool select by tag
OptionMin	runtime parameter for tool select by tag
optionType	runtime parameter for tool clean transcript file
distance	runtime parameter for tool clusterize
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
OptionDistance	runtime parameter for tool compare overlapping small query

Steps (44)

Name	Tool	Description
Input dataset	None
Input dataset	None
compare overlapping small query	toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/CompareOverlappingSmallQuery/1.0.0
compare overlapping small query	toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/CompareOverlappingSmallQuery/1.0.0
compare overlapping small query	toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/CompareOverlappingSmallQuery/1.0.0
Concatenate datasets	cat1
restrict from size	toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/restrictFromSize/1.0.0
restrict from size	toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/restrictFromSize/1.0.0
clusterize	toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/MergingDataClusterize/1.0.0
select by tag	toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/SelectByTag/1.0.0
select by tag	toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/SelectByTag/1.0.0
remove exon lines	toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/removeExonLines/1.0.0
clean transcript file	toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/CleanTranscriptFile/1.0.0
clusterize	toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/MergingDataClusterize/1.0.0
clusterize	toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/MergingDataClusterize/1.0.0
collapse reads	toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/collapseReads/1.0.0
remove exon lines	toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/removeExonLines/1.0.0
remove exon lines	toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/removeExonLines/1.0.0
splitTranscriptGff	toolshed.g2.bx.psu.edu/repos/clairetn/detrprok_scripts/splitTranscriptGff/1.0.0
change tag name	toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/changeTagName/1.0.0
change tag name	toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/changeTagName/1.0.0
compare overlapping small reference	toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/CompareOverlappingSmallRef/1.0.0
change GFF features	toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/changeGffFeatures/1.0.0
BAM-to-SAM	bam_to_sam
change GFF features	toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/changeGffFeatures/1.0.0
change tag name	toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/changeTagName/1.0.0
colorGff	toolshed.g2.bx.psu.edu/repos/clairetn/detrprok_scripts/colorGff/1.0.0
colorGff	toolshed.g2.bx.psu.edu/repos/clairetn/detrprok_scripts/colorGff/1.0.0
Extract features	Extract_features1
Extract features	Extract_features1
Extract features	Extract_features1
change GFF features	toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/changeGffFeatures/1.0.0
change GFF features	toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/changeGffFeatures/1.0.0
change GFF features	toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/changeGffFeatures/1.0.0
clusterize	toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/MergingDataClusterize/1.0.0
restrict from size	toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/restrictFromSize/1.0.0
select by tag	toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/SelectByTag/1.0.0
change GFF features	toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/changeGffFeatures/1.0.0
colorGff	toolshed.g2.bx.psu.edu/repos/clairetn/detrprok_scripts/colorGff/1.0.0
clusterize	toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/MergingDataClusterize/1.0.0
remove exon lines	toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/removeExonLines/1.0.0
remove exon lines	toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/removeExonLines/1.0.0
collapse reads	toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/collapseReads/1.0.0
compare overlapping small query	toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/CompareOverlappingSmallQuery/1.0.0

Outputs (42)

Name	Type
outputFileGff	gff3
outputFileGff	gff3
outputFileGff	gff3
out_file1	input
outputFileGff	gff3
outputFileGff	gff3
outputFileGff	gff3
outputFileGff	gff3
outputFileGff	gff3
outputFile	gff3
outputFile	gtf
outputFileGff	gff3
outputFileGff	gff3
outputFileGff	gff3
outputFile	gff3
outputFile	gff3
outputFile	gff3
outputFileGff	gff3
outputFileGff	gff3
outputFileGff	gff3
outputFile	gff
output1	sam
outputFile	gff
outputFileGff	gff3
outputFile	gff
outputFile	gff
out_file1	input
out_file1	input
out_file1	input
outputFile	gff
outputFile	gff
outputFile	gff
outputFileGff	gff3
outputFileGff	gff3
outputFileGff	gff3
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 1 (earliest) (of 4)

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Information Statistics

3951 viewings

1251 downloads

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Version History

In chronological order:

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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