Commit eb7a62b7 authored by Eendebak, Liset's avatar Eendebak, Liset
Browse files

Delete mapping

parent 50ec6ea4
#ftp.sra.ebi.ac.uk/vol1/run/ERR462/ERR4627(061)/201806(13.A-10R1)_R1.fastq.gz
#, "20180613.A-10R2"
SAMPLES = ["20180613.A-10R1", "20180613.A-10R2"]
rule all:
input:
expand("{sample}_hisat2.gtf", sample=SAMPLES)
#leaf 288 R4_2 has a different name
rule mapping:
input:
reads = "../transcriptome/{sample}_R1.fastq.gz",
index = "../Arabidopsis_thaliana/TAIR.1.ht2",
output:
"{sample}_hisat2.sam",
params:
index="../Arabidopsis_thaliana/TAIR",
shell:
"hisat2 -p 1 -x {params.index} -U {input.reads} -S {output}"
rule sort_sam: # works for both bowtie2 and hisat2
input:
"{sample}_hisat2.sam"
output:
"{sample}_hisat2.bam"
shell:
"samtools sort -o {output} {input}"
rule stringtie:
input:
bamfile = "{sample}_hisat2.bam",
annotation = "../Arabidopsis_thaliana/genes.gtf",
output:
"{sample}_hisat2.gtf"
params:
label="{sample}"
shell:
"stringtie -G {input.annotation} -o {output} -l {params.label} {input.bamfile}"
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