remove splice junction parameters for STAR to allow older versions to…

… run
hugp-ri · Dec 7, 2023 · de6cff9 · de6cff9
1 parent e2987ee
commit de6cff9
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/hicup_mapper b/hicup_mapper
@@ -440,8 +440,8 @@ sub map_file {
          $oid = open3( \*WRITER, \*READER, \*ERROR, "$config{hisat2} -x $config{index} --$config{format} -k 1 --no-unal --no-spliced-alignment --no-softclip --threads $bowtie2_threads --reorder - -S $outputfile" );
     } elsif ( $config{star} ne '' ) {
          print "\n running STAR...\n" unless $config{quiet};
-         print ( "\n $config{star} --runMode alignReads --genomeDir $config{index} --outQSconversionAdd $config{format} --readFilesIn /dev/stdin --runThreadN $bowtie2_threads --outSAMtype SAM --chimMainSegmentMultNmax 1 --chimSegmentMin 0 --outSJtype None --outFilterIntronMotifs  RemoveNoncanonical --outFilterIntronStrands RemoveInconsistentStrands --outFilterMismatchNmax 1 --outFilterMultimapNmax 1 --bamRemoveDuplicatesType UniqueIdentical --outSAMmultNmax 1 --alignSoftClipAtReferenceEnds No --alignEndsType EndToEnd --alignIntronMax 0  --alignIntronMin 999999999999 --outSAMunmapped None --outReadsUnmapped None --readFilesCommand cat --outFileNamePrefix $inputprefix --outStd SAM > $outputfile &&  \n" )  unless $config{quiet};
-         $oid = open3( \*WRITER, \*READER, \*ERROR, "$config{star} --runMode alignReads --genomeDir $config{index} --outQSconversionAdd $config{format} --readFilesIn /dev/stdin --runThreadN $bowtie2_threads --outSAMtype SAM --chimMainSegmentMultNmax 1 --chimSegmentMin 0 --outSJtype None --outFilterIntronMotifs  RemoveNoncanonical --outFilterIntronStrands RemoveInconsistentStrands --outFilterMismatchNmax 1 --outFilterMultimapNmax 1 --bamRemoveDuplicatesType UniqueIdentical --outSAMmultNmax 1 --alignSoftClipAtReferenceEnds No --alignEndsType EndToEnd --alignIntronMax 0 --alignIntronMin 999999999999 --outSAMunmapped None --outReadsUnmapped None --readFilesCommand cat --outFileNamePrefix $inputprefix --outStd SAM > $outputfile && cat ${inputprefix}Log.final.out | tr '\t' ' ' 1>&2" );
+         print ( "\n $config{star} --runMode alignReads --genomeDir $config{index} --outQSconversionAdd $config{format} --readFilesIn /dev/stdin --runThreadN $bowtie2_threads --outSAMtype SAM --chimMainSegmentMultNmax 1 --chimSegmentMin 0 --outFilterIntronMotifs  RemoveNoncanonical --outFilterMismatchNmax 1 --outFilterMultimapNmax 1 --bamRemoveDuplicatesType UniqueIdentical --outSAMmultNmax 1 --alignSoftClipAtReferenceEnds No --alignEndsType EndToEnd --alignIntronMax 0  --alignIntronMin 999999999999 --outSAMunmapped None --outReadsUnmapped None --readFilesCommand cat --outFileNamePrefix $inputprefix --outStd SAM > $outputfile &&  \n" )  unless $config{quiet};
+         $oid = open3( \*WRITER, \*READER, \*ERROR, "$config{star} --runMode alignReads --genomeDir $config{index} --outQSconversionAdd $config{format} --readFilesIn /dev/stdin --runThreadN $bowtie2_threads --outSAMtype SAM --chimMainSegmentMultNmax 1 --chimSegmentMin 0 --outFilterIntronMotifs  RemoveNoncanonical --outFilterMismatchNmax 1 --outFilterMultimapNmax 1 --bamRemoveDuplicatesType UniqueIdentical --outSAMmultNmax 1 --alignSoftClipAtReferenceEnds No --alignEndsType EndToEnd --alignIntronMax 0 --alignIntronMin 999999999999 --outSAMunmapped None --outReadsUnmapped None --readFilesCommand cat --outFileNamePrefix $inputprefix --outStd SAM > $outputfile && cat ${inputprefix}Log.final.out | tr '\t' ' ' 1>&2" );
     } else {
         print("Must path for specify at least one aligner: bowtie, bowtie2, dragen, hisat2, or star in configuration");
         exit(1);