From b11ab87b516219f23a9ca6a79750da18ab458bf7 Mon Sep 17 00:00:00 2001
From: burri0000 <dominik.burri@unibas.ch>
Date: Fri, 24 Jan 2020 12:13:10 +0100
Subject: [PATCH] test STAR and ALFA with chr21.bam
---
snakemake/Snakefile | 44 ++++++++++++++++++++++++++++++++++++++++----
1 file changed, 40 insertions(+), 4 deletions(-)
diff --git a/snakemake/Snakefile b/snakemake/Snakefile
index 84f043b..e9eee45 100644
--- a/snakemake/Snakefile
+++ b/snakemake/Snakefile
@@ -204,16 +204,52 @@ rule run_alfa_bg_stranded:
-o {output}
"""
+rule star_rpm_unstranded:
+ ''' Create unstranded bedgraph coverage with STARs RPM normalisation '''
+ input:
+ bam = "/scicore/home/zavolan/burri0000/test_alfa/sample/chr21.bam"
+ output:
+ "/scicore/home/zavolan/burri0000/rnaseqpipeline/snakemake/star_rpm/STAR_Signal.UniqueMultiple.str1.out.bg"
+ params:
+ out_dir = "/scicore/home/zavolan/burri0000/rnaseqpipeline/snakemake/star_rpm/",
+ filenameprefix = "/scicore/home/zavolan/burri0000/rnaseqpipeline/snakemake/star_rpm/STAR_"
+ singularity:
+ "docker://zavolab/star:2.6.0a"
+ threads: 4
+ log: "logs/star_rpm.log"
+ shell:
+ """
+ (mkdir -p {params.out_dir}; \
+ chmod -R 777 {params.out_dir}; \
+ STAR \
+ --runMode inputAlignmentsFromBAM \
+ --runThreadN {threads} \
+ --inputBAMfile {input.bam} \
+ --outWigType "bedGraph" \
+ --outWigStrand "Unstranded" \
+ --outWigNorm "RPM" \
+ --outFileNamePrefix {params.filenameprefix}) &> {log}
+ """
+
rule run_alfa_bg_unstranded:
''' Run ALFA from unstranded bedgraph files '''
input:
- "/scicore/home/zavolan/burri0000/test_alfa/sample/star_rpm/STAR_Signal.UniqueMultiple.str1.out.bg",
- "/scicore/home/zavolan/burri0000/test_alfa/sample/star_rpm/STAR_Signal.UniqueMultiple.str2.out.bg"
+ "/scicore/home/zavolan/burri0000/rnaseqpipeline/snakemake/star_rpm/STAR_Signal.UniqueMultiple.str1.out.bg"
output:
+ "/scicore/home/zavolan/burri0000/rnaseqpipeline/snakemake/star_rpm/ALFA_plots.Biotypes.pdf",
+ "/scicore/home/zavolan/burri0000/rnaseqpipeline/snakemake/star_rpm/ALFA_plots.Categories.pdf"
params:
- genome_index = "sorted_genes"
+ out_dir = "star_rpm",
+ in_file = "STAR_Signal.UniqueMultiple.str1.out.bg",
+ genome_index = "/scicore/home/zavolan/burri0000/rnaseqpipeline/snakemake/alfa_index/sorted_genes",
+ name = "test_chr21"
+ singularity:
+ "docker://zavolab/alfa:1.1.1"
+ log: "../logs/alfa_bg_unstranded.log"
shell:
"""
+ cd {params.out_dir}; \
alfa -g {params.genome_index} \
- -bedgraph {input} \
+ --bedgraph {params.in_file} {params.name} \
+ &> {log}
"""
\ No newline at end of file
--
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