From 9da923d496194717631fe01294807add476f2500 Mon Sep 17 00:00:00 2001 From: yuragal Date: Thu, 29 Dec 2016 19:06:36 +0800 Subject: [PATCH] Update align_rnaseq_gsnap.pl Without this flag, processing of input files containing filtered reads than could have no pair, result in error in GSNAP call. This error is similar to [this one](https://www.biostars.org/p/203212/). --- bin/align_rnaseq_gsnap.pl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bin/align_rnaseq_gsnap.pl b/bin/align_rnaseq_gsnap.pl index c695cd90..ba28c38c 100755 --- a/bin/align_rnaseq_gsnap.pl +++ b/bin/align_rnaseq_gsnap.pl @@ -523,7 +523,7 @@ () $file_align_cmd .= ' --gunzip ' if $file =~ /\.gz$/; $file_align_cmd .= $qual_prot if $qual_prot; - $file_align_cmd .= " --split-output=gsnap.$base --read-group-id=$base $file $pair "; + $file_align_cmd .= " --split-output=gsnap.$base --read-group-id=$base --allow-pe-name-mismatch $file $pair "; &process_cmd( $file_align_cmd, '.', "gsnap.$base*" ) unless ( -s "$base_out_filename"."_uniq" || -s "$base_out_filename"."_uniq.bam" ); unless ( -s "$base_out_filename"."_uniq.bam" || $just_write_out_commands) {