diff --git a/batchAlignment.pl b/batchAlignment.pl index 163ff05..585f942 100644 --- a/batchAlignment.pl +++ b/batchAlignment.pl @@ -87,7 +87,7 @@ ($$$$) " --runMode alignReads" . " --genomeDir $path_genome_index" . " --readFilesCommand zcat" . - " --outStdLog" . + " --outStd Log" . " --outSAMtype BAM SortedByCoordinate" . " --outSAMstrandField intronMotif" . " --outFilterIntronMotifs RemoveNoncanonical" .