diff --git a/Snakefile b/Snakefile
index 5a8e7ea80e84bc2ad8aebd261277c361e4c28328..450f545fb2fc330dd881f02e0ae8bb4ed3ec003e 100644
--- a/Snakefile
+++ b/Snakefile
@@ -394,20 +394,24 @@ rule extract_transcripts_as_bed12:
             "full_transcripts_protein_coding.bed")
 
     singularity:
-        "docker://zavolab/gtf_transcript_type_to_bed12:0.1.0-slim"
+        "docker://zavolab/zgtf:0.1"
 
     threads: 1
 
     log:
+        stdout = os.path.join(
+            config['log_dir'],
+            "extract_transcripts_as_bed12.stdout.log"),
         stderr = os.path.join(
             config['log_dir'],
             "extract_transcripts_as_bed12.stderr.log")
 
     shell:
-        "(gtf_transcript_type_to_bed12.pl \
-        --anno={input.gtf} \
-        --type=protein_coding > {output.bed12}); \
-        2> {log.stderr}"
+        "(gtf2bed12 \
+        --gtf {input.gtf} \
+        --transcript_type protein_coding \
+        --bed12 {output.bed12}); \
+        1> {log.stdout} 2> {log.stderr}"
 
 
 rule index_genomic_alignment_samtools:
diff --git a/workflow/rules/paired_end.snakefile.smk b/workflow/rules/paired_end.snakefile.smk
index d7f40dd71c1728c2bd7e3ddb6e02b86bd6d878c9..d66b120f1a03b787af23b27e96397cfd97e37117 100644
--- a/workflow/rules/paired_end.snakefile.smk
+++ b/workflow/rules/paired_end.snakefile.smk
@@ -228,7 +228,7 @@ rule pe_map_genome_star:
         --readFilesCommand zcat \
         --outSAMunmapped None  \
         --outFilterMultimapNmax {params.multimappers} \
-        --outFilterMultimapScoreRange 1 \
+        --outFilterMultimapScoreRange 0 \
         --outFileNamePrefix {params.outFileNamePrefix} \
         --outSAMattributes All \
         --outStd BAM_SortedByCoordinate \
diff --git a/workflow/rules/single_end.snakefile.smk b/workflow/rules/single_end.snakefile.smk
index e047aa40395946db666c70903684ebdce56afa26..41e506245b29cb8250e62c7a62d5353d3dc7c4ae 100644
--- a/workflow/rules/single_end.snakefile.smk
+++ b/workflow/rules/single_end.snakefile.smk
@@ -182,7 +182,7 @@ rule map_genome_star:
         --readFilesCommand zcat \
         --outSAMunmapped None  \
         --outFilterMultimapNmax {params.multimappers} \
-        --outFilterMultimapScoreRange 1 \
+        --outFilterMultimapScoreRange 0 \
         --outFileNamePrefix {params.outFileNamePrefix} \
         --outSAMattributes All \
         --outStd BAM_SortedByCoordinate \