From 226774cd2d0a735afd6be75866479dd285884159 Mon Sep 17 00:00:00 2001 From: BGI2015 Date: Mon, 27 Jul 2015 22:45:21 +0800 Subject: [PATCH] update20150727 --- .../RES-Scanner_identification.pl | 11 +++++-- .../bin/Amino_acid_change.pl | 6 ---- .../bin/RNA_edit_site_table.pl | 20 ++++++------- .../RES-Scanner_identification/bin/bigTable.pl | 2 +- .../bin/filter_abnormal_alignment_forBWA.pl | 2 +- .../bin/filter_edit_site_table.pl | 14 ++++----- .../RES-Scanner_identification/bin/findOverlap.pl | 5 ---- .../bin/findOverlap_sameStrand.pl | 5 ---- .../RES-Scanner_identification/bin/gtf2gff.pl | 33 --------------------- .../DNA_gynes_1.fq.gz} | Bin .../DNA_gynes_2.fq.gz} | Bin .../DNA_large_workers_1.fq.gz} | Bin .../DNA_large_workers_2.fq.gz} | Bin .../DNA_small_workers_1.fq.gz} | Bin .../DNA_small_workers_2.fq.gz} | Bin .../RNA_gyne_heads_1.fq.gz} | Bin .../RNA_gyne_heads_2.fq.gz} | Bin .../RNA_large_worker_heads_1.fq.gz} | Bin .../RNA_large_worker_heads_2.fq.gz} | Bin .../RNA_small_worker_heads_1.fq.gz} | Bin .../RNA_small_worker_heads_2.fq.gz} | Bin 21 files changed, 27 insertions(+), 71 deletions(-) delete mode 100644 RES-Scanner/RES-Scanner_identification/bin/gtf2gff.pl rename testData/fastq/DNA/{DNA_Ae322_gynes/DNA_Ae322_gynes_1.fq.gz => DNA_gynes/DNA_gynes_1.fq.gz} (100%) rename testData/fastq/DNA/{DNA_Ae322_gynes/DNA_Ae322_gynes_2.fq.gz => DNA_gynes/DNA_gynes_2.fq.gz} (100%) rename testData/fastq/DNA/{DNA_Ae322_large_workers/DNA_Ae322_large_workers_1.fq.gz => DNA_large_workers/DNA_large_workers_1.fq.gz} (100%) rename testData/fastq/DNA/{DNA_Ae322_large_workers/DNA_Ae322_large_workers_2.fq.gz => DNA_large_workers/DNA_large_workers_2.fq.gz} (100%) rename testData/fastq/DNA/{DNA_Ae322_small_workers/DNA_Ae322_small_workers_1.fq.gz => DNA_small_workers/DNA_small_workers_1.fq.gz} (100%) rename testData/fastq/DNA/{DNA_Ae322_small_workers/DNA_Ae322_small_workers_2.fq.gz => DNA_small_workers/DNA_small_workers_2.fq.gz} (100%) rename testData/fastq/RNA/{RNA_Ae322_gyne_heads/RNA_Ae322_gyne_heads_1.fq.gz => RNA_gyne_heads/RNA_gyne_heads_1.fq.gz} (100%) rename testData/fastq/RNA/{RNA_Ae322_gyne_heads/RNA_Ae322_gyne_heads_2.fq.gz => RNA_gyne_heads/RNA_gyne_heads_2.fq.gz} (100%) rename testData/fastq/RNA/{RNA_Ae322_large_worker_heads/RNA_Ae322_large_worker_heads_1.fq.gz => RNA_large_worker_heads/RNA_large_worker_heads_1.fq.gz} (100%) rename testData/fastq/RNA/{RNA_Ae322_large_worker_heads/RNA_Ae322_large_worker_heads_2.fq.gz => RNA_large_worker_heads/RNA_large_worker_heads_2.fq.gz} (100%) rename testData/fastq/RNA/{RNA_Ae322_small_worker_heads/RNA_Ae322_small_worker_heads_1.fq.gz => RNA_small_worker_heads/RNA_small_worker_heads_1.fq.gz} (100%) rename testData/fastq/RNA/{RNA_Ae322_small_worker_heads/RNA_Ae322_small_worker_heads_2.fq.gz => RNA_small_worker_heads/RNA_small_worker_heads_2.fq.gz} (100%) diff --git a/RES-Scanner/RES-Scanner_identification/RES-Scanner_identification.pl b/RES-Scanner/RES-Scanner_identification/RES-Scanner_identification.pl index 36ce349..daa65f1 100644 --- a/RES-Scanner/RES-Scanner_identification/RES-Scanner_identification.pl +++ b/RES-Scanner/RES-Scanner_identification/RES-Scanner_identification.pl @@ -44,6 +44,7 @@ "phred:s"=>\$phred, "DNAdepth:s"=>\$DNAdepth, "RNAdepth:s"=>\$RNAdepth, + "editDepth:s"=>\$readType, "posdir:s"=>\$posdir, "editLevel:s"=>\$editLevel, "editPvalue:s"=>\$pvalue, @@ -387,6 +388,10 @@ print STEP4RE "perl $Amino_acid_change $OutDir/RES_final_result.annotation $OutDir/codon.database > $OutDir/RES_final_result.annotation.temp\n"; print STEP4RE "mv -f $OutDir/RES_final_result.annotation.temp $OutDir/RES_final_result.annotation\n"; } + print STEP4RE "echo step4 work is completed! > $OutDir/step4.log\n"; + print STEP4RE "echo step4 work is completed!\n"; + print STEP4RE "echo File '$OutDir/RES_final_result.annotation' is the final result! >> $OutDir/step4.log\n"; + print STEP4RE "echo File '$OutDir/RES_final_result.annotation' is the final result!\n"; }else{ if($method eq "Bayesian"){ print STEP4RE "perl $bigTable --config $OutDir/bigTable.config --genome $genome --phred $phred --qual_cutoff $q --method $method --HomoPrior $HomoPrior --rate $rate --ploidy $ploidy --DNAdepth $DNAdepth --RNAdepth $RNAdepth --Bayesian_P $Bayesian_Posterior_Probability --paralogous_D $paralogous_D --homopolymer $homopolymer > $OutDir/RES_final_result.txt\n"; @@ -401,10 +406,12 @@ print STEP4RE "perl $filter_sites_in_paralogous_regions $OutDir/RES_final_result.txt.bilateral_sequence.fa.psl $OutDir/RES_final_result.txt > $OutDir/RES_final_result.txt.filter\n"; print STEP4RE "mv -f $OutDir/RES_final_result.txt.filter $OutDir/RES_final_result.txt\n"; } + print STEP4RE "echo step4 work is completed! > $OutDir/step4.log\n"; + print STEP4RE "echo step4 work is completed!\n"; + print STEP4RE "echo File '$OutDir/RES_final_result.txt' is the final result! >> $OutDir/step4.log\n"; + print STEP4RE "echo File '$OutDir/RES_final_result.txt' is the final result!\n"; } -print STEP4RE "echo step4 work is completed! > $OutDir/step4.log\n"; -print STEP4RE "echo step4 work is completed!\n"; close STEP4RE; print STDERR "####################################################################################################\n"; diff --git a/RES-Scanner/RES-Scanner_identification/bin/Amino_acid_change.pl b/RES-Scanner/RES-Scanner_identification/bin/Amino_acid_change.pl index 7e0a179..29a8f49 100644 --- a/RES-Scanner/RES-Scanner_identification/bin/Amino_acid_change.pl +++ b/RES-Scanner/RES-Scanner_identification/bin/Amino_acid_change.pl @@ -49,12 +49,6 @@ $CODE{$codon} = "*" unless (exists $CODE{$codon}); my $amino = $CODE{$codon}; my $C_a = join "$info[7]",$info[6],$amino; -# my $key; -# $key = 0 if ($info[6] eq $amino); -# $key = 1 if ($info[6] ne $amino); -# $key = -1 if ($amino eq "U" && $info[6] ne "U"); -# $key = 2 if ($amino ne "U" && $info[6] eq "U"); -# $result{$info[0]}{$info[1]}{$info[2]} = [$C_c,$C_a,$key]; $result{$info[0]}{$info[1]}{$info[2]} = [$C_c,$C_a]; } close IN; diff --git a/RES-Scanner/RES-Scanner_identification/bin/RNA_edit_site_table.pl b/RES-Scanner/RES-Scanner_identification/bin/RNA_edit_site_table.pl index f8288ca..d9e8bbd 100644 --- a/RES-Scanner/RES-Scanner_identification/bin/RNA_edit_site_table.pl +++ b/RES-Scanner/RES-Scanner_identification/bin/RNA_edit_site_table.pl @@ -7,7 +7,6 @@ my ($RNA_singleBase,$DNA_singleBase,$DNAdepth,$phred,$qual_cutoff,$RNAdepth,$editLevel,$editDepth,$strand,$RNA_bam,$ploidy,$samtools,$genome,$method); my $HomoPrior ||= 0.99; -my $HetePrior ||= 0.01; my $rate ||= 4; #the rate of transition over transversion #$DNAdepth ||= 7; #$RNAdepth ||= 3; @@ -33,7 +32,6 @@ "ploidy:s"=>\$ploidy, "samtools:s"=>\$samtools, "HomoPrior:s"=>\$HomoPrior, - "HetePrior:s"=>\$HetePrior, "rate:s"=>\$rate, "method:s"=>\$method, ); @@ -51,9 +49,8 @@ --strand The strand of data, '+' or '-' for strand specific data, 'unknown' for non-strand specific data. --ploidy The ploidy level, 1 for monoploid , 2 for diploid, 3 for triploid, 4 for tetraploid, and so on. [2]. --samtools The absolute path of pre-installed SAMtools package; - --method Method for detecting SNPs.'Bayesian' or 'Binomial' or 'Stringent'. [Bayesian] + --method Method for detecting SNPs.'Bayesian' or 'Binomial' or 'Frequency'. [Bayesian] --HomoPrior The prior probability of homozygous genomic positions. (force --method Bayesian) [0.99] - --HetePrior The prior probability of heterozygous genomic positions. (force --method Bayesian) [0.01] --rate The rate of transitions over transversions of the genome. (force --method Bayesian) [4] @@ -64,6 +61,7 @@ exit; } +my $HetePrior = 1-$HomoPrior; die "$RNA_singleBase does not exist!\n" unless -e $RNA_singleBase; die "$DNA_singleBase doesn't exist!\n" unless -e $DNA_singleBase; die "$samtools doesn't exist!\n" unless -e $samtools; @@ -73,8 +71,8 @@ die "Input Error: --strand should be '+' or '-' or 'unknown'!\n"; } -if($method ne "Bayesian" && $method ne "Binomial" && $method ne "Stringent"){ - die "Error: unknown options value '$method' for --Method [Bayesian|Binomial|Stringent]\n"; +if($method ne "Bayesian" && $method ne "Binomial" && $method ne "Frequency"){ + die "Error: unknown options value '$method' for --Method [Bayesian|Binomial|Frequency]\n"; }elsif($method eq "Bayesian" && !$genome){ die "Error: options --genome is undefined in Bayesian mode\n"; } @@ -194,8 +192,8 @@ }elsif($method eq "Binomial"){ @result = &SNPvalue_Binomial($dna_info,$ref_base,$ploidy); $homo{$info[0]}{$info[1]} = [$coverage,$ref_base,$dna_info,$result[0]]; - }elsif($method eq "Stringent"){ - @result = &SNPvalue_Stringent($seq,$ref_base); + }elsif($method eq "Frequency"){ + @result = &SNPvalue_Frequency($seq,$ref_base); $homo{$info[0]}{$info[1]} = [$coverage,$ref_base,$dna_info,$result[0],$result[1]]; }else{ die "Error: unknown --Method $method"; @@ -452,7 +450,7 @@ ($title1,$title2)=("Bayesian_Genotype(DNA)","Bayesian_Posterior_Probability(DNA)"); }elsif($method eq "Binomial"){ ($title1,$title2)=("P_value(DNA_Heterozygosis)","FDR(DNA_Heterozygosis)"); -}elsif($method eq "Stringent"){ +}elsif($method eq "Frequency"){ ($title1,$title2)=("Non_Ref_BaseCount(DNA)","Non_Ref_BaseRatio(DNA)"); }else{ die "Error: unknown --Method $method\n"; @@ -467,7 +465,7 @@ } $time= &getTime(); -print STDERR "$time\tRaw candidate RNA editing sites is generated.!\n"; +print STDERR "$time\tRaw candidate RNA editing sites is generated!\n"; ## @@ -715,7 +713,7 @@ sub SNPvalue_Binomial{ } -sub SNPvalue_Stringent{ +sub SNPvalue_Frequency{ my ($s,$r)=@_; my @S=split //,$s; my $totalDep=@S; diff --git a/RES-Scanner/RES-Scanner_identification/bin/bigTable.pl b/RES-Scanner/RES-Scanner_identification/bin/bigTable.pl index a8cc321..42c9bae 100644 --- a/RES-Scanner/RES-Scanner_identification/bin/bigTable.pl +++ b/RES-Scanner/RES-Scanner_identification/bin/bigTable.pl @@ -5,7 +5,6 @@ use Getopt::Long; my ($config,$phred,$qual_cutoff,$genome,$intron,$homopolymer,$paralogous_D); my $HomoPrior ||= 0.99; -my $HetePrior = 1-$HomoPrior; my $rate ||= 2; #the rate of transition over transversion my $method ||= "Bayesian"; my $ploidy ||= 2; @@ -74,6 +73,7 @@ }elsif($method eq "Bayesian" && !$genome){ die "Error: options --genome is undefined in Bayesian mode\n"; } +my $HetePrior = 1-$HomoPrior; my %hash; my @order; open IN,"$config" or die $!; diff --git a/RES-Scanner/RES-Scanner_identification/bin/filter_abnormal_alignment_forBWA.pl b/RES-Scanner/RES-Scanner_identification/bin/filter_abnormal_alignment_forBWA.pl index e817dea..972140e 100644 --- a/RES-Scanner/RES-Scanner_identification/bin/filter_abnormal_alignment_forBWA.pl +++ b/RES-Scanner/RES-Scanner_identification/bin/filter_abnormal_alignment_forBWA.pl @@ -57,7 +57,7 @@ system "mv $outdir/temp.$n.$filename $outBamfile"; }else{ # print STDERR "Log: There is no ambiguous mapping between BWA and BLAT!\n"; - system "ln -s $inBamfile $outBamfile"; + system "ln -sf $inBamfile $outBamfile"; } diff --git a/RES-Scanner/RES-Scanner_identification/bin/filter_edit_site_table.pl b/RES-Scanner/RES-Scanner_identification/bin/filter_edit_site_table.pl index a8ff6c2..cbf9f8a 100644 --- a/RES-Scanner/RES-Scanner_identification/bin/filter_edit_site_table.pl +++ b/RES-Scanner/RES-Scanner_identification/bin/filter_edit_site_table.pl @@ -29,8 +29,8 @@ "Bayesian_P:s"=>\$Bayesian_Posterior_Probability, "Binomial_P:s"=>\$P_value_DNA_Heterozygosis, "Binomial_FDR:s"=>\$FDR_DNA_Heterozygosis, - "Stringent_N:s"=>\$Non_Ref_BaseCount, - "Stringent_R:s"=>\$Non_Ref_BaseRatio, + "Frequency_N:s"=>\$Non_Ref_BaseCount, + "Frequency_R:s"=>\$Non_Ref_BaseRatio, "editPvalue:s"=>\$p, "help"=>\$help, ); @@ -42,18 +42,18 @@ --DNAdepth The homozygous DNA depth [optional(default:7)] --RNAdepth The minimum cutoff for RNA reads coverage. [3] --editLevel The minimum cutoff for editing level. [0.05] - --method Method for detecting SNPs.'Bayesian' or 'Binomial' or 'Stringent'. [Bayesian] + --method Method for detecting SNPs.'Bayesian' or 'Binomial' or 'Frequency'. [Bayesian] --Bayesian_P The minimun Bayesian Posterior Probability cutoff for corresponding genotype.(force --method Bayesian) [0.95] --Binomial_P The maximun P value cutoff of Binomial test for DNA Heterozygosis. (force --method Binomial) [0.05] --Binomial_FDR The maximun FDR cutoff of Binomial test for DNA Heterozygosis. (force --method Binomial) [0.05] - --Stringent_N The maximun non-refference base count cutoff. (force --method Stringent) [0] - --Stringent_R The maximun non-refference base ratio cutoff. (force --method Stringent) [0] + --Frequency_N The maximun non-refference base count cutoff. (force --method Frequency) [0] + --Frequency_R The maximun non-refference base ratio cutoff. (force --method Frequency) [0] --readType The least number of RNA reads that were mapped to overlapping but not identical positions in the reference genome that supporting an RNA-editing site in a given sample. [3] --goodRead The least number of RNA reads which in the middle of their length supporting an editing site (that is, from positions 26~75 of the 100-bp read), to avoid potential false positives resulting from mis-mapping of reads at splice junctions. [1] - --editPvalue Cutoff of FDR RNA editing. [0.05] + --editPvalue Cutoff of FDR RNA editing. [0.05] --help Show the help information. @@ -85,7 +85,7 @@ }elsif($method eq "Binomial"){ next unless $label1<$P_value_DNA_Heterozygosis; next unless $label2<$FDR_DNA_Heterozygosis; - }elsif($method eq "Stringent"){ + }elsif($method eq "Frequency"){ next if $label1>$Non_Ref_BaseCount; next if $label2>$Non_Ref_BaseRatio; }else{ diff --git a/RES-Scanner/RES-Scanner_identification/bin/findOverlap.pl b/RES-Scanner/RES-Scanner_identification/bin/findOverlap.pl index 5ad89b3..5c4c1f3 100644 --- a/RES-Scanner/RES-Scanner_identification/bin/findOverlap.pl +++ b/RES-Scanner/RES-Scanner_identification/bin/findOverlap.pl @@ -20,11 +20,6 @@ Column 8: the first subject block ame.Group4.17 overlapped with ame.Group1.64, + is the strand of ame.Group4.17, 326 is its own size, 209 is the overlapped size; Column 9: the second subject block ame.Group16.8 overlapped with ame.Group1.64, - is the strand of ame.Group16.8, numbers has the same meaning as last column; -Version: - - Author: jinlijun, jinlijun\@genomics.org.cn - Version: 1.0, Date: 2011-05-18 - Usage perl findOverlap.pl [pre] diff --git a/RES-Scanner/RES-Scanner_identification/bin/findOverlap_sameStrand.pl b/RES-Scanner/RES-Scanner_identification/bin/findOverlap_sameStrand.pl index a265bd8..9372c2d 100644 --- a/RES-Scanner/RES-Scanner_identification/bin/findOverlap_sameStrand.pl +++ b/RES-Scanner/RES-Scanner_identification/bin/findOverlap_sameStrand.pl @@ -20,11 +20,6 @@ Column 8: the first subject block ame.Group4.17 overlapped with ame.Group1.64, + is the strand of ame.Group4.17, 326 is its own size, 209 is the overlapped size; Column 9: the second subject block ame.Group16.8 overlapped with ame.Group1.64, + is the strand of ame.Group16.8, numbers has the same meaning as last column; -Version: - - Author: jinlijun, jinlijun\@genomics.org.cn - Version: 1.0, Date: 2011-05-18 - Usage perl findOverlap.pl [pre] diff --git a/RES-Scanner/RES-Scanner_identification/bin/gtf2gff.pl b/RES-Scanner/RES-Scanner_identification/bin/gtf2gff.pl deleted file mode 100644 index b42ed67..0000000 --- a/RES-Scanner/RES-Scanner_identification/bin/gtf2gff.pl +++ /dev/null @@ -1,33 +0,0 @@ -#!/usr/bin/perl -w -use strict; -die "Usage: \n" unless @ARGV == 1; - -my %cdsPos; -if ($ARGV[0] =~ /\.gz$/) { - open IN, "gunzip -c $ARGV[0] | "; -} else { - open IN, $ARGV[0]; -} -while () { - chomp; - next if /^#/; - my @info = split /\t/; - if ($info[1] !~ "pseudogene" && $info[2] eq "CDS") { - die "Warning: Unrecognized gff format, 'transcript_id' is missing." unless $info[-1] =~ /transcript_id\s+"(\S+)\s?";/; - my $transcript_id = $1; - my ($geneID)= $info[-1] =~ /gene_id\s+"(\S+)\s?";/; - ($info[3], $info[4]) = sort {$a <=> $b}($info[3], $info[4]); - push @{$cdsPos{$transcript_id}}, [$info[3], $info[4], $info[0], $info[6], $info[7], $geneID]; - } -} -close IN; - -foreach my $transcript (keys %cdsPos) { - @{$cdsPos{$transcript}} = sort {$a->[0] <=> $b->[0]} @{$cdsPos{$transcript}}; - my ($transcript_bg, $transcript_ed, $chr, $strand, $geneID) = ($cdsPos{$transcript}->[0]->[0], $cdsPos{$transcript}->[-1]->[1], $cdsPos{$transcript}->[0]->[2], $cdsPos{$transcript}->[0]->[3],$cdsPos{$transcript}->[0]->[5]); - print "$chr\tensembl\tmRNA\t$transcript_bg\t$transcript_ed\t.\t$strand\t.\tID=$transcript;GeneID=$geneID\n"; - foreach my $p (@{$cdsPos{$transcript}}) { - my ($cds_bg, $cds_ed, $chr, $strand, $phase) = @$p; - print "$chr\tensembl\tCDS\t$cds_bg\t$cds_ed\t.\t$strand\t$phase\tParent=$transcript;GeneID=$geneID\n"; - } -} diff --git a/testData/fastq/DNA/DNA_Ae322_gynes/DNA_Ae322_gynes_1.fq.gz b/testData/fastq/DNA/DNA_gynes/DNA_gynes_1.fq.gz similarity index 100% rename from testData/fastq/DNA/DNA_Ae322_gynes/DNA_Ae322_gynes_1.fq.gz rename to testData/fastq/DNA/DNA_gynes/DNA_gynes_1.fq.gz diff --git a/testData/fastq/DNA/DNA_Ae322_gynes/DNA_Ae322_gynes_2.fq.gz b/testData/fastq/DNA/DNA_gynes/DNA_gynes_2.fq.gz similarity index 100% rename from testData/fastq/DNA/DNA_Ae322_gynes/DNA_Ae322_gynes_2.fq.gz rename to testData/fastq/DNA/DNA_gynes/DNA_gynes_2.fq.gz diff --git a/testData/fastq/DNA/DNA_Ae322_large_workers/DNA_Ae322_large_workers_1.fq.gz b/testData/fastq/DNA/DNA_large_workers/DNA_large_workers_1.fq.gz similarity index 100% rename from testData/fastq/DNA/DNA_Ae322_large_workers/DNA_Ae322_large_workers_1.fq.gz rename to testData/fastq/DNA/DNA_large_workers/DNA_large_workers_1.fq.gz diff --git a/testData/fastq/DNA/DNA_Ae322_large_workers/DNA_Ae322_large_workers_2.fq.gz b/testData/fastq/DNA/DNA_large_workers/DNA_large_workers_2.fq.gz similarity index 100% rename from testData/fastq/DNA/DNA_Ae322_large_workers/DNA_Ae322_large_workers_2.fq.gz rename to testData/fastq/DNA/DNA_large_workers/DNA_large_workers_2.fq.gz diff --git a/testData/fastq/DNA/DNA_Ae322_small_workers/DNA_Ae322_small_workers_1.fq.gz b/testData/fastq/DNA/DNA_small_workers/DNA_small_workers_1.fq.gz similarity index 100% rename from testData/fastq/DNA/DNA_Ae322_small_workers/DNA_Ae322_small_workers_1.fq.gz rename to testData/fastq/DNA/DNA_small_workers/DNA_small_workers_1.fq.gz diff --git a/testData/fastq/DNA/DNA_Ae322_small_workers/DNA_Ae322_small_workers_2.fq.gz b/testData/fastq/DNA/DNA_small_workers/DNA_small_workers_2.fq.gz similarity index 100% rename from testData/fastq/DNA/DNA_Ae322_small_workers/DNA_Ae322_small_workers_2.fq.gz rename to testData/fastq/DNA/DNA_small_workers/DNA_small_workers_2.fq.gz diff --git a/testData/fastq/RNA/RNA_Ae322_gyne_heads/RNA_Ae322_gyne_heads_1.fq.gz b/testData/fastq/RNA/RNA_gyne_heads/RNA_gyne_heads_1.fq.gz similarity index 100% rename from testData/fastq/RNA/RNA_Ae322_gyne_heads/RNA_Ae322_gyne_heads_1.fq.gz rename to testData/fastq/RNA/RNA_gyne_heads/RNA_gyne_heads_1.fq.gz diff --git a/testData/fastq/RNA/RNA_Ae322_gyne_heads/RNA_Ae322_gyne_heads_2.fq.gz b/testData/fastq/RNA/RNA_gyne_heads/RNA_gyne_heads_2.fq.gz similarity index 100% rename from testData/fastq/RNA/RNA_Ae322_gyne_heads/RNA_Ae322_gyne_heads_2.fq.gz rename to testData/fastq/RNA/RNA_gyne_heads/RNA_gyne_heads_2.fq.gz diff --git a/testData/fastq/RNA/RNA_Ae322_large_worker_heads/RNA_Ae322_large_worker_heads_1.fq.gz b/testData/fastq/RNA/RNA_large_worker_heads/RNA_large_worker_heads_1.fq.gz similarity index 100% rename from testData/fastq/RNA/RNA_Ae322_large_worker_heads/RNA_Ae322_large_worker_heads_1.fq.gz rename to testData/fastq/RNA/RNA_large_worker_heads/RNA_large_worker_heads_1.fq.gz diff --git a/testData/fastq/RNA/RNA_Ae322_large_worker_heads/RNA_Ae322_large_worker_heads_2.fq.gz b/testData/fastq/RNA/RNA_large_worker_heads/RNA_large_worker_heads_2.fq.gz similarity index 100% rename from testData/fastq/RNA/RNA_Ae322_large_worker_heads/RNA_Ae322_large_worker_heads_2.fq.gz rename to testData/fastq/RNA/RNA_large_worker_heads/RNA_large_worker_heads_2.fq.gz diff --git a/testData/fastq/RNA/RNA_Ae322_small_worker_heads/RNA_Ae322_small_worker_heads_1.fq.gz b/testData/fastq/RNA/RNA_small_worker_heads/RNA_small_worker_heads_1.fq.gz similarity index 100% rename from testData/fastq/RNA/RNA_Ae322_small_worker_heads/RNA_Ae322_small_worker_heads_1.fq.gz rename to testData/fastq/RNA/RNA_small_worker_heads/RNA_small_worker_heads_1.fq.gz diff --git a/testData/fastq/RNA/RNA_Ae322_small_worker_heads/RNA_Ae322_small_worker_heads_2.fq.gz b/testData/fastq/RNA/RNA_small_worker_heads/RNA_small_worker_heads_2.fq.gz similarity index 100% rename from testData/fastq/RNA/RNA_Ae322_small_worker_heads/RNA_Ae322_small_worker_heads_2.fq.gz rename to testData/fastq/RNA/RNA_small_worker_heads/RNA_small_worker_heads_2.fq.gz