config.yaml

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# Settings for paired-end

# Correspondance to ISR library type
# https://salmon.readthedocs.io/en/latest/library_type.html
# the recommended default --fr for Illumina works
# Do not report discordant or only single mate mapping
# Suppress SAM records for reads that failed to align.
# Also, use fragment size larger than the 500 default
bowtie_pe: "--fr --no-discordant --no-mixed --no-unal --maxins 700"
# (p)aired, (B)oth ends,  check (P)airs
# reverse (s)trand
# -D 700 for larger fragment size
#
# Note: Please do not set '-s 2' here, which is controlled by 'reverse' column
#       in samples.csv.
featurecount_pe: "--fracOverlap 0.5 --largestOverlap -p -B -P -D 700 -F SAF"

# 30 mapq corersponds to probability of mapping to other position 0.001
filter_pe: "-f bam -F 'proper_pair and not unmapped and mapping_quality >= 30'"

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# Settings for single-end

# Correspondance to SR library type by salmon
# https://salmon.readthedocs.io/en/latest/library_type.html
bowtie_se: ""
# Note: Please do not set '-s 2' here, which is controlled by 'reverse' column
#       in samples.csv.
featurecount_se: "--fracOverlap 0.5 --largestOverlap -F SAF"

# 30 mapq corersponds to probability of mapping to other position 0.001
filter_se: "-f bam -F 'not unmapped and mapping_quality >= 30'"

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# Browser

# Under which URL you wish to publish to have the browser accessible
deploy_url: 'http://localhost:3000'

# Release URL of Jbrowser to use
jbrowse_url: 'https://github.com/GMOD/jbrowse-components/releases/download/v2.10.0/jbrowse-web-v2.10.0.zip'

# short id for browser, suggestion: Use the KEGG organism identifier
browser_short: 'xyz'
browser_name: 'RNA-seq browser'

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