NGS : RNAseq workflow part 1 from Tophat to filtered SAM

Created: 2014-03-04 10:36:53 Last updated: 2014-06-10 09:17:03

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Remove duplicates from Tophat BAM output files and filter

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Inputs (1)

Name	Description
BAM file from Tophat	Remove duplicate from a Tophat output BAM file then filter

Steps (5)

Name	Tool	Description
Input dataset	None
rmdup	toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/1.0.0
BAM-to-SAM	toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/1.0.3
Filter SAM	toolshed.g2.bx.psu.edu/repos/devteam/sam_bitwise_flag_filter/sam_bw_filter/1.0.0
Filter	testtoolshed.g2.bx.psu.edu/repos/greg/gregs_filter/Filter1/3.3.0

Outputs (4)

Name	Type
output1	bam
output1	sam
out_file1	sam
out_file1	input

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Galaxy

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Ylebras

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Ylebras

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992 viewings

645 downloads

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Citations (1)Version History

1. Y. Le Bras, A. Roult, C. Monjeaud, M. Bahin, O. Quenez, C. Heriveau, A. Bretaudeau, O. Sallou, O. Collin, Towards a Life Sciences Virtual Research Environment : an e-Science initiative in Western France, JOBIM 2013, 03 July 2013, https://www.e-biogenouest.org/resources/128

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