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config
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--------------------------------MANDATORY INPUTS--------------------------------
################################################################################
Path and basename of the genome index to be searched. The basename is the name
of any of the index files up to but not including the final .1.ebwt/.rev.1.ebwt
/etc.
index=
############################## ANNOTATION ######################################
Path to annotation file in GFF3/GTF format. File should contain non coding
annotation.
annotation=
################################################################################
Path to reference FASTA/FA genome file.
genome=
------------------------------NON-MANDATORY INPUTS------------------------------
################################################################################
Path and basename of the transcriptome index to be searched. The basename is the
name of any of the index files up to but not including the final .1.ebwt/
.rev.1.ebwt/etc. If left blank, spipeRNA will generate the transcriptome index
based on provided annotation file and will store it within the trabscripts
directory.
t_index=
################################################################################
Maximun number of mismatches in genomic alignments (default: mismatches=1).
mismatches=1
################################################################################
Number of alignment cores (default: cores=1).
cores=1
################################################################################
Max of multimapping loci, -m in bowtie execution. The mapping algorithm will be
applied only for reads with multi-mapped loci less or equal than -m. Reads with
multimapped loci that exceed the m will be aligned against transcriptome
(default: m=50).
m=50
################################################################################
Strand specific mode of the algorithm. Possible values yes/no (default: s=yes).
s=yes
################################################################################
Collapse reads with the same genomic sequence. This setting reduces signifi-
cantly the execution time. Possible values yes/no (default: collapse=yes).
collapse=yes
################################################################################
Minimum number of unannotated read abundances per cluster (default: cd=5).
cd=5
################################################################################
Clusters of unannotated reads will be merged if the distance between them is
equal or less than cdi (default: cdi=50).
cdi=50