Commit b9d4b867 authored by Molemaker, Maureen's avatar Molemaker, Maureen
Browse files

added docstring and index_bam rule, also added -e to the stringtie command

parent ed411cd0
......@@ -3,7 +3,7 @@ Author: Maureen Molemaker, studentnumber
Author: Liset Eendebak, studentnumber 1014355
script to map the fastq reads onto the reference genome
and to annotate the transcripts
Usage: snakemake -s mapping -c 1 # use 1 core
Usage: snakemake -s mapping -c <no. of cores>
"""
SAMPLES = ["20180613.A-13R1", "20180613.A-13R2", "20180613.A-13R3",
......@@ -42,6 +42,14 @@ rule sort_sam: # works for both bowtie2 and hisat2
shell:
"samtools sort -o {output} {input}"
#This rule was used for validating the mapping in IGV
#rule index_bam: # works for both bowtie2 and hisat2
# input:
# "{sample}_hisat2.bam"
# output:
# "{sample}_hisat2.bam.bai"
# shell:
# "samtools index {input}"
rule gene_annotation:
input:
......@@ -52,7 +60,7 @@ rule gene_annotation:
params:
label="{sample}"
shell:
"stringtie -G {input.annotation} -o {output} -l {params.label} {input.bamfile}"
"stringtie -G {input.annotation} -e -o {output} -l {params.label} {input.bamfile}"
......
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