clean up

README.md

@@ -452,3 +452,4 @@ For any of the listed reasons, or anything else, please leave us a <a href="http
 
 <a href="https://github.com/srobb1/RelocaTE/issues?page=1&sort=comments&state=open">Leave a message here</a>
 
+

sample_relocaTE_run/sample_readme.txt

@@ -9,6 +9,7 @@ These scripts expect that the following programs are installed and included in y
 	3. BWA
 	4. BioPerl
    	5. Blat
+	6. Blast: formatdb and fastacmd
 
 STEPS A-C
 A. RelocaTE
@@ -32,32 +33,32 @@ A. To find TE insertions in the included fastq reads run RelocaTE:
         or
         sh run_relocaTE.sh
 
-   These scritps will run relocaTE directly or through a series of shell scripts. 
-        If you are running
+  These scripts will run relocaTE directly or through a series of shell scripts. 
+	If you are running
         - run_relocaTE_qsub.sh:
-                1) follow the instructions that are printed to the screen (run run_these_jobs.sh)
-                2) once complete, view the results in 02052012_sample/mping/results
+		1) follow the instructions that are printed to the screen (run run_these_jobs.sh)
+      		2) once complete, view the results in 02052012_sample/mping/results
         or
         - run_relocaTE_shell.sh
-                1) follow the instructions that are printed to the screen (run run_these_jobs.sh)
-                2) once complete, view the results in 02052012_sample/mping/results
+		1) follow the instructions that are printed to the screen (run run_these_jobs.sh)
+      		2) once complete, view the results in 02052012_sample/mping/results
         or
         - run_relocaTE.sh
-                1) once complete, view the results in 02052012_sample/mping/results
+      		1) once complete, view the results in 02052012_sample/mping/results
 
 
-B. Find Spanners to help classify the insertions (homozygous, heterozygous, etc) by generating a BAM file of the reads not trimmed of TE to the referenc
-e.
+B. Find Spanners to help classify the insertions (homozygous, heterozygous, etc) by generating a BAM file of the reads not trimmed of TE to the reference.
   A BAM file is included in the sample data set, but one can be genreted by running the included script:
-        create_bam.sh by:
-        - changing directory into the directory of this script
-        - and typing "sh create_bam.sh"
+	create_bam.sh by:
+	- changing directory into the directory of this script
+ 	- and typing "sh create_bam.sh"
 
 
 C. To classify the insertions (homozygous, heterozygous, etc) run_characTErizer.sh 
-        - change directory into the directory of this script
-        - type "sh run_characTErizer.sh"
+	- change directory into the directory of this script
+	- type "sh run_characTErizer.sh"
         - once complete, view the resulting files in the directory you ran characTErizer.pl
-                1) sample.inserts_characTErized.gff: GFF file of the classified insertions including excisions 
-                2) sample.inserts_characTErized.txt: Text file of the classified insertions including excisions
-                3) excisions_with_footprint.vcfinfo: additional information on the insertions that have been classified as exicision events 
+		1) sample.inserts_characTErized.gff: GFF file of the classified insertions including excisions 
+		2) sample.inserts_characTErized.txt: Text file of the classified insertions including excisions
+		3) excisions_with_footprint.vcfinfo: additional information on the insertions that have been classified as exicision events  
+

scripts/characterizer.pl

@@ -310,3 +310,4 @@ sub getHelp {
     }
   }
 }
+

scripts/relocaTE.pl

@@ -147,8 +147,8 @@
 }
 else {
   my $fq_path = File::Spec->rel2abs($fq_dir);
-  @fq_files = <$fq_path/*fq>;
-  my @fastq_files = <$fq_path/*fastq>;
+  @fq_files = <$fq_path/*.fq>;
+  my @fastq_files = <$fq_path/*.fastq>;
   push @fq_files, @fastq_files;
   if ( scalar @fq_files == 0 ) {
     print "Must provide at least 1 short read file\n";