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rule.smk
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rule.smk
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rule hisat2:
input:
# Required input.
alignment = '{sample}.sorted.bam',
annotation = 'reference/gencode.v28.gtf.gz'
output:
'result/{sample}/{sample}.htseq_count.result'
threads: 1
params:
# Optional parameters. Read through the comments carefully.
# Provide appropriate option for your data,
# or comment out the option if it is not needed.
extra = '',
# Mode to handle reads overlapping more thain one feature.
# CANDIDATES: union, intersection-strict, intersection-nonempty
# DEFAULT: union
mode = 'union',
# Whether the data is from a strand-specific assay.
# CANDIDATES: yes, no, reverse
# DEFAULT: yes
# NOTE: Use reverse for the data generated recently.
stranded = 'reverse'
log: 'logs/htseq/count/{sample}.log'
wrapper:
'http://dohlee-bio.info:9193/hisat2'