Skip to content

Updated hisat2_align.pl #9

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
Kapeel wants to merge 1 commit into
base: master
Choose a base branch
from
Open

Updated hisat2_align.pl #9

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
10 changes: 4 additions & 6 deletions hisat2/2.0.5/Hisat2_align.pl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@
use Getopt::Long qw(:config no_ignore_case no_auto_abbrev pass_through);

my (@file_query, $database_path, $user_database_path, $annotation_path,
$user_annotation_path, $file_names, $root_names, @file_query2, $lib_type, $file_type, $n_cores);
$user_annotation_path, $file_names, $root_names, @file_query2, $file_type, $n_cores);


GetOptions( "file_query=s" => \@file_query,
Expand All @@ -16,7 +16,6 @@
"user_annotation=s" => \$user_annotation_path,
"file_names=s" => \$file_names,
"root_names=s" => \$root_names,
"lib_type=s" => \$lib_type,
"file_type=s" => \$file_type,
"n_cores=s" => \$n_cores,
);
Expand Down Expand Up @@ -71,13 +70,12 @@

my $app = "/usr/bin/hisat2";
my $format = $file_type;
my $library = $lib_type;

chomp(my $basename = `basename $query_file`);
$basename =~ s/\.\S+$//;

if ($format eq "PE") {
my $align_command = "$app $HISAT_ARGS --rna-strandness $library -x $name -1 $query_file -2 $second_file -p $n_cores | samtools view -bS - > $query_file.bam";
my $align_command = "$app $HISAT_ARGS -x $name -1 $query_file -2 $second_file -p $n_cores | samtools view -bS - > $query_file.bam";
report("Executing: $align_command\n");
system $align_command;
system "samtools sort $query_file.bam $basename.sorted";
Expand All @@ -86,7 +84,7 @@
system "rm -rf *bam";
}
elsif($format eq "SE"){
my $align_command = "$app $HISAT_ARGS --rna-strandness $library -x $name -U $query_file -p $n_cores | samtools view -bS - > $query_file.bam";
my $align_command = "$app $HISAT_ARGS -x $name -U $query_file -p $n_cores | samtools view -bS - > $query_file.bam";
report("Executing: $align_command\n");
system $align_command;
system "samtools sort $query_file.bam $basename.sorted";
Expand All @@ -101,4 +99,4 @@

sub report {
print STDERR "$_[0]\n";
}
}