From 21fe79681c1491dd6838b6b152dc935580bc9eb2 Mon Sep 17 00:00:00 2001
From: mariabernard <maria.bernard@jouy.inra.fr>
Date: Wed, 19 Jun 2019 12:57:24 +0200
Subject: [PATCH] 1000RNASEQ chicken ASE: correct wildcard constraint, rmdup
command line and add fasta index as input in SplitCigar
---
Snakemake/1000RNASeq_chicken/ASE/rules/STAR.smk | 12 ++++++++----
1 file changed, 8 insertions(+), 4 deletions(-)
diff --git a/Snakemake/1000RNASeq_chicken/ASE/rules/STAR.smk b/Snakemake/1000RNASeq_chicken/ASE/rules/STAR.smk
index 4ffd456..315f8d7 100644
--- a/Snakemake/1000RNASeq_chicken/ASE/rules/STAR.smk
+++ b/Snakemake/1000RNASeq_chicken/ASE/rules/STAR.smk
@@ -8,7 +8,7 @@ Align RNASeq reads on masked genome
'''
wildcard_constraints:
- properlyPaired_rmDup = '_pp_|_'
+ properlyPaired = '_pp_|_'
STAR_INDEX_FILE=['genomeParameters.txt', 'chrName.txt', 'chrLength.txt', 'chrStart.txt', 'chrNameLength.txt', 'exonGeTrInfo.tab', 'geneInfo.tab', 'transcriptInfo.tab', 'exonInfo.tab', 'sjdbList.fromGTF.out.tab', 'sjdbInfo.txt', 'sjdbList.out.tab', 'Genome', 'SA', 'SAindex']
@@ -157,18 +157,20 @@ def get_properly_paired_bam(wildcards):
return "Results/STAR_Aln_2/" + wildcards.sample + "_rg_genomic.bam"
+# note : This tool uses the READ_NAME_REGEX and the OPTICAL_DUPLICATE_PIXEL_DISTANCE options as the primary methods to identify and differentiate duplicate types. Set READ_NAME_REGEX to null to skip optical duplicate detection, e.g. for RNA-seq or other data where duplicate sets are extremely large and estimating library complexity is not an aim
+
rule RmDuplicates:
input:
bam = get_properly_paired_bam
output:
- bam = "Results/STAR_Aln_2/{sample}_rg_genomic{properlyPaired}.bam",
+ bam = "Results/STAR_Aln_2/{sample}_rg_genomic{properlyPaired}rmdup.bam",
metrics = "Results/STAR_Aln_2/{sample}_rg_genomic{properlyPaired}.metrics.txt",
params:
mem=str(int(config["rmdup"]["mem"].replace("G","")) -4 )+"G" if int(config["rmdup"]["mem"].replace("G","")) -4 > 1 else config["rmdup"]["mem"] ,
jar=find_jar("picard.jar")
shell:
"""
- java -Xmx{params.mem} -jar {params.jar} MarkDuplicates READ_NAME_REGEX=null I={input.bam} O={output.bam} REMOVE_DUPLICATES=true CREATE_INDEX=true VALIDATION_STRINGENCY=SILENT M={output.metrics}
+ java -Xmx{params.mem} -jar {params.jar} MarkDuplicates CREATE_INDEX=false READ_NAME_REGEX=null I={input.bam} O={output.bam} REMOVE_DUPLICATES=true VALIDATION_STRINGENCY=SILENT M={output.metrics}
"""
rule remove_multimap:
@@ -184,9 +186,11 @@ rule remove_multimap:
rule SplitNCigarReads:
input:
fasta = 'Results/genomeMasked/' + os.path.splitext(os.path.basename(config['fasta_ref']))[0] + '_masked.fa',
+ idx = 'Results/genomeMasked/' + os.path.splitext(os.path.basename(config['fasta_ref']))[0] + '_masked.fa.fai',
+ dict = 'Results/genomeMasked/' + os.path.splitext(os.path.basename(config['fasta_ref']))[0] + '_masked.dict',
bam = "Results/STAR_Aln_2/{sample}_rg_genomic{properlyPaired}rmdup_uniq.bam"
output:
- bam = "Results/STAR_Aln_2/{sample}_rg_genomic{properlyPairedrmdup_uniq_split.bam"
+ bam = "Results/STAR_Aln_2/{sample}_rg_genomic{properlyPaired}rmdup_uniq_split.bam"
params:
mem=config["SplitNCigarReads"]["mem"],
jar=find_jar("GenomeAnalysisTK.jar")
--
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