1000RNASEQ chicken ASE: add fasta dict and bam indexes in SplitNCigar rule

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

@@ -188,7 +188,8 @@ rule SplitNCigarReads:
         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"
+        bam = "Results/STAR_Aln_2/{sample}_rg_genomic{properlyPaired}rmdup_uniq.bam",
+        bai = "Results/STAR_Aln_2/{sample}_rg_genomic{properlyPaired}rmdup_uniq.bai"
     output:
         bam = "Results/STAR_Aln_2/{sample}_rg_genomic{properlyPaired}rmdup_uniq_split.bam"
     params:

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

@@ -52,5 +52,5 @@ rule indexFasta:
 	shell:
 		"""
 		samtools faidx {input.ref}
-        java -Xmx{params.mem} -jar {params.jar} R={input.ref} O={output.dict}
+        java -Xmx{params.mem} -jar {params.jar} CreateSequenceDictionary R={input.ref} O={output.dict}
 		"""