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Remove sample specific options and use them as rule specific.

Merged BIOPZ-Katsantoni Maria requested to merge restructure_sample_table into dev
7 files
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@@ -160,6 +160,12 @@ map_genome_star:
@@ -160,6 +160,12 @@ map_genome_star:
# "SJ.out.tab" (default 'Normal', ZARP recommends 'BySJout', as this
# "SJ.out.tab" (default 'Normal', ZARP recommends 'BySJout', as this
# reduces the number of spurious junctions )
# reduces the number of spurious junctions )
--outFilterType: 'BySJout'
--outFilterType: 'BySJout'
 
# type of read ends alignment: force end-to-end read alignment, do not soft-clip
 
--alignEndsType: 'EndToEnd'
 
# extract junctions, insert them into the genome index and re-map reads in a 2nd mapping pass
 
--twopassMode: Basic
 
# alignments (all of them) will be output only if the read maps to no more loci than 10
 
--outFilterMultimapNmax: '10'
pe_map_genome_star:
pe_map_genome_star:
# The score range below the maximum score for multimapping alignments
# The score range below the maximum score for multimapping alignments
@@ -169,6 +175,12 @@ pe_map_genome_star:
@@ -169,6 +175,12 @@ pe_map_genome_star:
# "SJ.out.tab" (default 'Normal', ZARP recommends 'BySJout', as this
# "SJ.out.tab" (default 'Normal', ZARP recommends 'BySJout', as this
# reduces the number of spurious junctions )
# reduces the number of spurious junctions )
--outFilterType: 'BySJout'
--outFilterType: 'BySJout'
 
# type of read ends alignment: force end-to-end read alignment, do not soft-clip
 
--alignEndsType: 'EndToEnd'
 
# extract junctions, insert them into the genome index and re-map reads in a 2nd mapping pass
 
--twopassMode: Basic
 
# alignments (all of them) will be output only if the read maps to no more loci than 10
 
--outFilterMultimapNmax: '10'
quantification_salmon:
quantification_salmon:
# Correct for sequence specific biases; cf.
# Correct for sequence specific biases; cf.
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