RTTS Mapper

Created: 2012-07-17 17:28:52 Last updated: 2012-07-17 17:36:03

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Generates RTTS counts file from SAM file. Output consists of three columns: counts at given position;chromosome;position(0 based). Workflow removes untemplated nucleotides from 5' ends of the reads. Authors: Jeppe Vinther, Lukasz Kielpinski

Workflow published by lukaszkielpinski on Galaxy Jun 26, 2012 imported to myExperiment Jul 17, 2012 during demonstration of Galaxy-myExperiment integration (specifically generating SVG and showing steps of more complex workflow).

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Workflow Components

Inputs (0)

Steps (27)

Name	Tool	Description
Convert SAM	sam2interval
Filter	Filter1
Select	Grep1
Subtract Whole Dataset	subtract_query1
Compute	Add_a_column1
Subtract Whole Dataset	subtract_query1
Compute	Add_a_column1
Select	Grep1
Select	Grep1
Subtract Whole Dataset	subtract_query1
Compute	Add_a_column1
Subtract Whole Dataset	subtract_query1
Filter	Filter1
Compute	Add_a_column1
Compute	Add_a_column1
Compute	Add_a_column1
Concatenate datasets	cat1
Concatenate datasets	cat1
Count	Count1
Count	Count1
Select	Grep1
Select	Grep1
Subtract Whole Dataset	subtract_query1
Compute	Add_a_column1
Subtract Whole Dataset	subtract_query1
Compute	Add_a_column1
Select	Grep1

Outputs (27)

Name	Type
out_file1	interval
out_file1	input
out_file1	input
output	input
out_file1	input
output	input
out_file1	input
out_file1	input
out_file1	input
output	input
out_file1	input
output	input
out_file1	input
out_file1	input
out_file1	input
out_file1	input
out_file1	input
out_file1	input
out_file1	tabular
out_file1	tabular
out_file1	input
out_file1	input
output	input
out_file1	input
output	input
out_file1	input
out_file1	input