# HG changeset patch
# User romaingred
# Date 1511881552 18000
# Node ID af4ee65eaffb3b091ff20c5a51c389c53cfe5364
# Parent  dfe259eb1e6b03429c323c70fa0ad173b0d8fe3c
Uploaded

diff -r dfe259eb1e6b -r af4ee65eaffb bin/piPipe.pl
--- a/bin/piPipe.pl	Tue Nov 28 09:24:35 2017 -0500
+++ b/bin/piPipe.pl	Tue Nov 28 10:05:52 2017 -0500
@@ -203,7 +203,7 @@
 			extract_sam ( $type_sequence_hashP, $sam_genome, $type_sam_genome, $type_sam_uni_genome, $type_genome_fastq, $type_uni_genome_fastq );
 		}
 
-		my $ex_count_file =  $type_dir.'transcripts_reads_counts.txt';
+		my $ex_count_file =  $type_dir.$type_prefix.'transcripts_reads_counts.txt';
 		my ( $ex_count, $ex_ref_size ) =  sam_count ( $type_sam_transcripts );
 		rpms_rpkm( $ex_count, $ex_ref_size, $ma, $ex_count_file, $pi, $mi, $bo );
 
@@ -253,7 +253,7 @@
 
 	#HTML Main Webpage
 	my $index_page = $dir.$fastq_n[$child].'.html';
-  main_page ( $gen_dir, $index_page, \@fastq_n, $fastq_n[$child], $ma, $ma_uni, $dir );
+	main_page ( $gen_dir, $index_page, \@fastq_n, $fastq_n[$child], $ma, $ma_uni, $dir );
   copy ($index_page, $html_out) if $child == 0;
 	#HTML Menu
 	my $menu_page = $dir.$fastq_n[$child].'-sub.html';