1000RNASeq_chicken ASE : perform rmdup for single end read

Snakemake/1000RNASeq_chicken/ASE/Snakefile

@@ -130,7 +130,7 @@ for sample in table["sample_name"].unique():
 	    final_outputs.append("Results/STAR_Aln_2/" + sample + "_rg_genomic_pp_rmdup_uniq_split.bam")
 	# single end, no filter on properly paired
 	elif len(sample_table["reverse_read"].dropna() ) == 0:
-	    final_outputs.append("Results/STAR_Aln_2/" + sample + "_rg_genomic_uniq_split.bam")
+	    final_outputs.append("Results/STAR_Aln_2/" + sample + "_rg_genomic_rmdup_uniq_split.bam")
 
 # # counter
 for sample in table["sample_name"].unique():
@@ -146,4 +146,4 @@ for sample in table["sample_name"].unique():
 
 rule all:
     input:
-        final_outputs
\ No newline at end of file
+        final_outputs

Snakemake/1000RNASeq_chicken/ASE/rules/ASE_counter.smk

@@ -18,7 +18,7 @@ def get_splitNCigar_bam(wildcards):
         return "Results/STAR_Aln_2/" + wildcards.sample + "_rg_genomic_pp_rmdup_uniq_split.bam"
     # single end, no filter
     elif len(sample_table["reverse_read"].dropna() ) == 0:
-        return "Results/STAR_Aln_2/" + wildcards.sample + "_rg_genomic_uniq_split.bam"
+        return "Results/STAR_Aln_2/" + wildcards.sample + "_rg_genomic_rmdup_uniq_split.bam"
     else :
     	raise Exception(wildcards.sample + " is sequenced in pair end & single end mode\n 	This workflow do not accept this case!\n")
 

Snakemake/1000RNASeq_chicken/ASE/rules/STAR.smk

@@ -8,7 +8,7 @@ Align RNASeq reads on masked genome
 '''
 
 wildcard_constraints:
-    properlyPaired_rmDup = '_pp_rmdup_|_'
+    properlyPaired_rmDup = '_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']
 
@@ -161,8 +161,8 @@ rule rmdup:
     input:
         bam = get_properly_paired_bam
     output:
-        bam = "Results/STAR_Aln_2/{sample}_rg_genomic{properlyPaired_rmDup}.bam",
-        metrics = "Results/STAR_Aln_2/{sample}_rg_genomic{properlyPaired_rmDup}.metrics.txt",
+        bam = "Results/STAR_Aln_2/{sample}_rg_genomic{properlyPaired}.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")
@@ -173,9 +173,9 @@ rule rmdup:
 
 rule remove_multimap:
     input:
-        bam = "Results/STAR_Aln_2/{sample}_rg_genomic{properlyPaired_rmDup}.bam"
+        bam = "Results/STAR_Aln_2/{sample}_rg_genomic{properlyPaired}rmdup.bam"
     output:
-        bam = "Results/STAR_Aln_2/{sample}_rg_genomic{properlyPaired_rmDup}uniq.bam"
+        bam = "Results/STAR_Aln_2/{sample}_rg_genomic{properlyPaired}rmdup_uniq.bam"
     shell:
         """
         samtools view -h -q 255 {input.bam} -bo {output.bam} 
@@ -184,9 +184,9 @@ rule remove_multimap:
 rule SplitNCigarReads:
     input:
         fasta = 'Results/genomeMasked/' + os.path.splitext(os.path.basename(config['fasta_ref']))[0] + '_masked.fa', 
-        bam = "Results/STAR_Aln_2/{sample}_rg_genomic{properlyPaired_rmDup}uniq.bam"
+        bam = "Results/STAR_Aln_2/{sample}_rg_genomic{properlyPaired}rmdup_uniq.bam"
     output:
-        bam = "Results/STAR_Aln_2/{sample}_rg_genomic{properlyPaired_rmDup}uniq_split.bam"
+        bam = "Results/STAR_Aln_2/{sample}_rg_genomic{properlyPairedrmdup_uniq_split.bam"
     params:
         mem=config["SplitNCigarReads"]["mem"],
         jar=find_jar("GenomeAnalysisTK.jar")
@@ -194,4 +194,4 @@ rule SplitNCigarReads:
         """
         java -Xmx{params.mem} -jar {params.jar} -T SplitNCigarReads -R {input.fasta} -I {input.bam} -o {output.bam} -rf ReassignOneMappingQuality -RMQF 255 -RMQT 60 -U ALLOW_N_CIGAR_READS 
         """
-    
\ No newline at end of file
+