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xryanglab · Jun 13, 2020 · c2f888c · c2f888c
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diff --git a/README.md b/README.md
@@ -29,6 +29,8 @@ The **RiboMiner** is a python toolset for mining multi-dimensional features of t
 
 + All transcripts used on this package are the longest trancript of all protein coding genes.
 
++ Codes to reproduce the results presented in the paper are presented in [**Implementation**](https://github.com/xryanglab/RiboMiner/blob/master/Implementation.md) file or published in [**CodeOcean**](https://codeocean.com/capsule/3780896/tree/v1) for repeatability analysis.
+
 # **Dependencies**
 
 + matplotlib>=2.1.0
@@ -151,6 +153,14 @@ LengthDistribution -i <sequence_sample.bam> -o <output_prefix> -f bam
 ```
 where *sequence_sample.fastq* is the fastq file after adapter trimmed and filtered with sequence quality and *sequence_sample.bam* is the mapping file. This step would generate two files. One is the plot of length distribution with *pdf* format and the other is the length of each sequencing read.
 
+If users want to display length distribution of reads from differnet regions (CDS, 5'UTR, 3'UTR) or calculate reads length for specific transcripts, ***ReadsLengthOfSpecificRegions*** would be helpful.
+
+```
+usage:
+ReadsLengthOfSpecificRegions -i bamFile  -c longest.transcripts.info.txt -o output_prefix --type CDS/5UTR/3UTR { -S transcript_list --id-type transcript_id}
+
+```
+
 + **DNA contamination.**
 
 Sometimes the length distribution of ribosome footprint is biased away from 28nt-30nt, which is the normal length distribution of ribosome profiling data. Therefore, this step aims to statistic numbers of the reads mapped to RNA, DNA, Intron region,and re-check the length distriution of reads mapped to transcriptome.
@@ -167,6 +177,14 @@ unique mapped ambiguous reads of RNA: 119989
 ```
 The other three are *pdf* files, which are length distribution plot of reads mapped to RNA, DNA, and Intron.  Notes: this step would consume a lot of time, aroumd 10~20 minutes.
 
++ **Read counting**
+
+```
+Usage:
+ModifyHTseq -i bamFile -g gtfFile -o countsFile -t exon -m union -q 10 --minLen 25 --maxLen 35 --exclude-first 45 --exclude-last 15 --id-type gene_id
+Notes: This script only used for strand specific library.
+```
+
 
 
 ## **Metagene Analysis (MA)**

diff --git a/RuningTimeTest/Fly/code/DivideGeneSets.R b/RuningTimeTest/Fly/code/DivideGeneSets.R
@@ -0,0 +1,17 @@
+all_mean_density <- read.table("../results/MetageneAnalysis/test_all_local_mean_density.txt",sep="\t",stringsAsFactors = F,header = T,check.names = F)
+all_mean_density_non_zeros <- all_mean_density[Reduce(intersect,lapply(all_mean_density,function(x){which(x>0)})),]
+#all_mean_density_non_zeros['Ctrl'] <- (all_mean_density_non_zeros$`Ctrl-1`+all_mean_density_non_zeros$`Ctrl-2`)/2
+all_mean_density_non_zeros['Low-detergent'] <- all_mean_density_non_zeros$`Low-detergent-2`
+all_mean_density_non_zeros['High-detergent'] <- all_mean_density_non_zeros$`High-detergent-2`
+#all_mean_density_non_zeros['ASNase'] <- (all_mean_density_non_zeros$`ASNase-1`+all_mean_density_non_zeros$`ASNase-2`)/2
+all_mean_density_non_zeros['FC(High-detergent/Low-detergent)'] <- all_mean_density_non_zeros$`High-detergent`/all_mean_density_non_zeros$`Low-detergent`
+colnames(all_mean_density_non_zeros)[1] <- "trans_id"
+
+FC_le_0.67 <- all_mean_density_non_zeros[all_mean_density_non_zeros$`FC(High-detergent/Low-detergent)`<=0.67,]
+FC_ge_1.5 <- all_mean_density_non_zeros[all_mean_density_non_zeros$`FC(High-detergent/Low-detergent)`>=1.5,]
+FC_lt1.5_gt0.67 <- all_mean_density_non_zeros[all_mean_density_non_zeros$`FC(High-detergent/Low-detergent)`<1.5&all_mean_density_non_zeros$`FC(High-detergent/Low-detergent)`>0.67,]
+
+write.table(FC_le_0.67,"../results/MetageneAnalysis/down_trans.txt",quote = F,sep="\t",row.names = F,col.names = T)
+write.table(FC_ge_1.5,"../results/MetageneAnalysis/up_trans.txt",quote = F,sep="\t",row.names = F,col.names = T)
+write.table(FC_lt1.5_gt0.67,"../results/MetageneAnalysis/unblocked_trans.txt",quote = F,sep="\t",row.names = F,col.names = T)
+
diff --git a/RuningTimeTest/Fly/code/EA.sh b/RuningTimeTest/Fly/code/EA.sh
@@ -0,0 +1,32 @@
+#########################################################################
+# File Name: EA.sh
+# Author: lifj
+# mail: [email protected]
+# Created Time: Tue 09 Jun 2020 02:48:15 PM CST
+#########################################################################
+#!/bin/bash
+#BSUB -J EA.sh
+#BSUB -o EA.out
+#BSUB -e EA.err
+#BSUB -n 1
+#BSUB -q TEST-A
+
+
+results=../results
+
+mkdir -p $results/EnrichmentAnalysis
+
+RiboDensityAtEachPosition -c ../results/Ref/longest.transcripts.info.txt -f ../data/attributes.txt -o $results/EnrichmentAnalysis/test  -U codon
+
+#enrichmentMeanDensity -i $results/EnrichmentAnalysis/test_Ctrl-1_cds_codon_density.txt,$results/EnrichmentAnalysis/test_Ctrl-2_cds_codon_density.txt -o $results/EnrichmentAnalysis/Ctrl
+#enrichmentMeanDensity -i $results/EnrichmentAnalysis/test_ASNase-1_cds_codon_density.txt,$results/EnrichmentAnalysis/test_ASNase-2_cds_codon_density.txt -o $results/EnrichmentAnalysis/ASNase
+
+
+EnrichmentAnalysis --ctrl $results/EnrichmentAnalysis/test_Low-detergent-2_cds_codon_density.txt --treat $results/EnrichmentAnalysis/test_High-detergent-2_cds_codon_density.txt -c ../results/Ref/longest.transcripts.info.txt -o $results/EnrichmentAnalysis/test -U codon -M RPKM -l 150 -n 10 -m 1 -e 30 --CI 0.95 -u 0 -d 500
+
+#EnrichmentAnalysis --ctrl $results/EnrichmentAnalysis/test_Ctrl-1_cds_codon_density.txt --treat $results/EnrichmentAnalysis/eIF5A_si-eIF5A-2_cds_codon_density.txt -c ../results/Ref/longest.transcripts.info.extended.txt -o $results/EnrichmentAnalysis/eIF5A -U codon -M RPKM -l 150 -n 10 -m 1 -e 30 --CI 0.95 -u 0 -d 500
+
+
+
+
+
diff --git a/RuningTimeTest/Fly/code/FA.sh b/RuningTimeTest/Fly/code/FA.sh
@@ -0,0 +1,53 @@
+#########################################################################
+# File Name: FA.sh
+# Author: lifj
+# mail: [email protected]
+# Created Time: Tue 09 Jun 2020 02:47:59 PM CST
+#########################################################################
+#!/bin/bash
+#BSUB -J FA.sh
+#BSUB -o FA.out
+#BSUB -e FA.err
+#BSUB -n 1
+#BSUB -q TEST-A
+
+
+
+results=../results
+
+mkdir -p $results/FeatureAnalysis
+
+RiboDensityAtEachKindAAOrCodon -f ../data/attributes.txt -c ../results/Ref/longest.transcripts.info.txt -o ../results/FeatureAnalysis/up -M RPKM -S ../results/up_common_trans.txt -l 100 -n 10 --table 1 -F ../results/Ref/longest_cds_sequences.fa
+RiboDensityAtEachKindAAOrCodon -f ../data/attributes.txt -c ../results/Ref/longest.transcripts.info.txt -o ../results/FeatureAnalysis/down -M RPKM -S ../results/down_common_trans.txt -l 100 -n 10 --table 1 -F ../results/Ref/longest_cds_sequences.fa
+RiboDensityAtEachKindAAOrCodon -f ../data/attributes.txt -c ../results/Ref/longest.transcripts.info.txt -o ../results/FeatureAnalysis/unblocked -M RPKM -S ../results/unblocked_common_trans.txt -l 100 -n 10 --table 1 -F ../results/Ref/longest_cds_sequences.fa
+PlotRiboDensityAtEachKindAAOrCodon -i ../results/FeatureAnalysis/up_all_codon_density.txt -o ../results/FeatureAnalysis/up -g low-detergent,high-detergent -r Low-detergent-2__High-detergent-2 --level codon
+PlotRiboDensityAtEachKindAAOrCodon -i ../results/FeatureAnalysis/up_all_codon_density.txt -o ../results/FeatureAnalysis/up -g low-detergent,high-detergent -r Low-detergent-2__High-detergent-2 --level AA
+PlotRiboDensityAtEachKindAAOrCodon -i ../results/FeatureAnalysis/down_all_codon_density.txt -o ../results/FeatureAnalysis/down -g low-detergent,high-detergent -r Low-detergent-2__High-detergent-2 --level codon
+PlotRiboDensityAtEachKindAAOrCodon -i ../results/FeatureAnalysis/down_all_codon_density.txt -o ../results/FeatureAnalysis/down -g low-detergent,high-detergent -r Low-detergent-2__High-detergent-2 --level AA
+
+PausingScore -f ../data/attributes.txt -c ../results/Ref/longest.transcripts.info.txt -o ../results/FeatureAnalysis/up -M RPKM -S ../results/up_common_trans.txt -l 100 -n 10 --table 1 -F ../results/Ref/longest_cds_sequences.fa
+ProcessPausingScore -i ../results/FeatureAnalysis/up_Low-detergent-2_pausing_score.txt,../results/FeatureAnalysis/up_High-detergent-2_pausing_score.txt -o ../results/FeatureAnalysis/up -g low-detergent,high-detergent -r Low-detergent-2__High-detergent-2 --mode raw --ratio_filter 1.5 --pausing_score_filter 0.5
+
+conda activate python27
+./seq2logo-2.1/Seq2Logo.py -f ../results/FeatureAnalysis/up_pwm.txt  -u probability -I 5 -o ../results/FeatureAnalysis/up --format PDF
+conda deactivate
+
+RiboDensityAroundTripleteAAMotifs -f ../data/attributes.txt -c ../results/Ref/longest.transcripts.info.txt -o ../results/FeatureAnalysis/up_DD -M RPKM -S ../results/up_common_trans.txt -l 100 -n 10 --table 1 -F ../results/Ref/longest_cds_sequences.fa --type2 DDD --type1 DD
+RiboDensityAroundTripleteAAMotifs -f ../data/attributes.txt -c ../results/Ref/longest.transcripts.info.txt -o ../results/FeatureAnalysis/up_PP -M RPKM -S ../results/up_common_trans.txt -l 100 -n 10 --table 1 -F ../results/Ref/longest_cds_sequences.fa --type2 PPP --type1 PP
+RiboDensityAroundTripleteAAMotifs -f ../data/attributes.txt -c ../results/Ref/longest.transcripts.info.txt -o ../results/FeatureAnalysis/up_KK -M RPKM -S ../results/up_common_trans.txt -l 100 -n 10 --table 1 -F ../results/Ref/longest_cds_sequences.fa --type2 KKK --type1 KK
+
+PlotRiboDensityAroundTriAAMotifs -i ../results/FeatureAnalysis/up_PP_motifDensity_dataframe.txt -o ../results/FeatureAnalysis/up_PPP -g low-detergent,high-detergent -r Low-detergent-2__High-detergent-2 --mode mean --ymax 0.2
+PlotRiboDensityAroundTriAAMotifs -i ../results/FeatureAnalysis/up_DD_motifDensity_dataframe.txt -o ../results/FeatureAnalysis/up_DDD -g low-detergent,high-detergent -r Low-detergent-2__High-detergent-2 --mode mean --ymax 0.2  
+PlotRiboDensityAroundTriAAMotifs -i ../results/FeatureAnalysis/up_KK_motifDensity_dataframe.txt -o ../results/FeatureAnalysis/up_KKK -g low-detergent,high-detergent -r Low-detergent-2__High-detergent-2  --mode mean --ymax 0.2
+
+bash GetCdsSeqForGeneSets.sh
+tAI -i ../results/Ref/up_cds_sequences.fa,../results/Ref/down_cds_sequences.fa,../results/Ref/unblocked_cds_sequences.fa -N ../data/tRNA_GCNs_fly.txt -o ../results/FeatureAnalysis/test -u 0 -d 500 -t up-regulated-genes,down-regulated-genes,unblocked-genes
+cAI -i ../results/Ref/up_cds_sequences.fa,../results/Ref/down_cds_sequences.fa,../results/Ref/unblocked_cds_sequences.fa -o  ../results/FeatureAnalysis/test -u 0 -d 500 -t up-regulated-genes,down-regulated-genes,unblocked-genes --reference ../results/Ref/longest_cds_sequences.fa
+
+hydropathyCharge -i ../results/Ref/up_cds_sequences.fa,../results/Ref/down_cds_sequences.fa,../results/Ref/unblocked_cds_sequences.fa -t up-regulated-genes,down-regulated-genes,unblocked-genes -o ../results/FeatureAnalysis/test_hydropathy -u 0 -d 500 --index ../data/hydropathy.txt
+hydropathyCharge -i ../results/Ref/up_cds_sequences.fa,../results/Ref/down_cds_sequences.fa,../results/Ref/unblocked_cds_sequences.fa -t up-regulated-genes,down-regulated-genes,unblocked-genes -o ../results/FeatureAnalysis/test_Charge -u 0 -d 500 --index ../data/AA_charge.txt
+
+PlotHydropathyCharge -i ../results/FeatureAnalysis/test_Charge_values_dataframe.txt -o ../results/FeatureAnalysis/test_charge -u 0 -d 500 --mode all --ylab "Average Charges"
+PlotHydropathyCharge -i ../results/FeatureAnalysis/test_hydropathy_values_dataframe.txt -o ../results/FeatureAnalysis/test_hydro -u 0 -d 500 --mode all --ylab "Average Hydrophobicity"
+cAIPlot -i ../results/FeatureAnalysis/test_local_cAI_dataframe.txt -o ../results/FeatureAnalysis/test_cAI -u 0 -d 500 --mode all --start 5 --window 7 --step 1
+tAIPlot -i ../results/FeatureAnalysis/test_tAI_dataframe.txt -o ../results/FeatureAnalysis/test_tAI -u 0 -d 500 --mode all --start 5 --window 7 --step 1
diff --git a/RuningTimeTest/Fly/code/GetCdsSeqForGeneSets.sh b/RuningTimeTest/Fly/code/GetCdsSeqForGeneSets.sh
@@ -0,0 +1,15 @@
+#########################################################################
+# File Name: GetCdsSeqForGeneSets.sh
+# Author: lifj
+# mail: [email protected]
+# Created Time: Fri 01 May 2020 06:26:21 PM CST
+#########################################################################
+#!/bin/bash
+
+
+GetProteinCodingSequence -i ../results/Ref/RiboCode_annot/transcripts_sequence.fa  -c ../results/Ref/longest.transcripts.info.txt -o ../results/Ref/up  --mode whole --table 1  -S ../results/up_common_trans.txt
+GetProteinCodingSequence -i ../results/Ref/RiboCode_annot/transcripts_sequence.fa  -c ../results/Ref/longest.transcripts.info.txt -o ../results/Ref/down  --mode whole --table 1  -S ../results/down_common_trans.txt
+GetProteinCodingSequence -i ../results/Ref/RiboCode_annot/transcripts_sequence.fa  -c ../results/Ref/longest.transcripts.info.txt -o ../results/Ref/unblocked  --mode whole --table 1  -S ../results/unblocked_common_trans.txt
+
+
+
diff --git a/RuningTimeTest/Fly/code/GetCommonGeneSets.R b/RuningTimeTest/Fly/code/GetCommonGeneSets.R
@@ -0,0 +1,16 @@
+up_genes <- read.table("../results/MetageneAnalysis/test_up_CDS_normed_transcript_id.txt",sep="\t",stringsAsFactors = F,header = T,check.names = F)
+up_genes_common <- as.data.frame(Reduce(intersect,up_genes))
+
+down_genes <- read.table("../results/MetageneAnalysis/test_down_CDS_normed_transcript_id.txt",sep="\t",stringsAsFactors = F,header = T,check.names = F)
+down_genes_common <- as.data.frame(Reduce(intersect,down_genes))
+
+unblocked_genes <- read.table("../results/MetageneAnalysis/test_unblocked_CDS_normed_transcript_id.txt",sep="\t",stringsAsFactors = F,header = T,check.names = F)
+unblocked_genes_common <- as.data.frame(Reduce(intersect,unblocked_genes))
+
+colnames(up_genes_common) <- "trans_id"
+colnames(down_genes_common) <- "trans_id"
+colnames(unblocked_genes_common) <- "trans_id"
+
+write.table(up_genes_common,"../results/up_common_trans.txt",quote = F,sep="\t",row.names = F,col.names = T)
+write.table(down_genes_common,"../results/down_common_trans.txt",quote = F,sep="\t",row.names = F,col.names = T)
+write.table(unblocked_genes_common,"../results/unblocked_common_trans.txt",quote = F,sep="\t",row.names = F,col.names = T)
diff --git a/RuningTimeTest/Fly/code/MA.sh b/RuningTimeTest/Fly/code/MA.sh
@@ -0,0 +1,40 @@
+#########################################################################
+# File Name: MA.sh
+# Author: lifj
+# mail: [email protected]
+# Created Time: Tue 09 Jun 2020 02:47:46 PM CST
+#########################################################################
+#!/bin/bash
+#BSUB -J MA.sh
+#BSUB -o MA.out
+#BSUB -e MA.err
+#BSUB -n 1
+#BSUB -q TEST-A
+
+
+results=../results
+mkdir -p $results/MetageneAnalysis
+
+MetageneAnalysisForTheWholeRegions -f ../data/attributes.txt -c ../results/Ref/longest.transcripts.info.txt -o $results/MetageneAnalysis/test -b 15,90,15 -l 100 -n 10 -m 1 -e 5 
+
+PlotMetageneAnalysisForTheWholeRegions -i $results/MetageneAnalysis/test_scaled_density_dataframe.txt -o $results/MetageneAnalysis/test_whole -g low-detergent,high-detergent -r Low-detergent-2__High-detergent-2 -b 15,90,15 --mode all
+
+MetageneAnalysis -f ../data/attributes.txt -c ../results/Ref/longest.transcripts.info.txt -o $results/MetageneAnalysis/test_CDS_normed -U codon -M RPKM -u 0 -d 500 -l 100 -n 10 -m 1 -e 5 --norm yes -y 100 --CI 0.95 --type CDS
+MetageneAnalysis -f ../data/attributes.txt -c ../results/Ref/longest.transcripts.info.txt -o $results/MetageneAnalysis/test_UTR_normed -U nt -M RPKM -u 50 -d 50 -l 50 -n 10 -m 1 -e 5 --norm yes -y 50 --CI 0.95 --type UTR
+
+PolarityCalculation -f ../data/attributes.txt -c ../results/Ref/longest.transcripts.info.txt -o $results/MetageneAnalysis/test -n 64
+PlotMetageneAnalysis -i $results/MetageneAnalysis/test_CDS_normed_dataframe.txt -o $results/MetageneAnalysis/test_CDS_normed -g low-detergent,high-detergent -r Low-detergent-2__High-detergent-2 -U codon -u 0 -d 500 --mode mean --CI 0.95 --axhline 1
+
+PlotMetageneAnalysis -i $results/MetageneAnalysis/test_UTR_normed_dataframe.txt -o $results/MetageneAnalysis/test_UTR_normed -g low-detergent,high-detergent -r Low-detergent-2__High-detergent-2 -U nt -u 50 -d 50 --mode mean --CI 0.95 --axhline 1
+
+PlotPolarity -i  $results/MetageneAnalysis/test_polarity_dataframe.txt -o $results/MetageneAnalysis/test -g low-detergent,high-detergent -r Low-detergent-2__High-detergent-2 -y 5 --mode all
+
+RiboDensityForSpecificRegion -f ../data/attributes.txt -c ../results/Ref/longest.transcripts.info.txt -o $results/MetageneAnalysis/test_all -U codon -M RPKM -L 1 -R 100
+
+Rscript DivideGeneSets.R
+
+MetageneAnalysis -f ../data/attributes.txt -c ../results/Ref/longest.transcripts.info.txt -o $results/MetageneAnalysis/test_up_CDS_normed -U codon -M RPKM -u 0 -d 500 -l 100 -n 5 -m 1 -e 5 --norm yes -y 100 --CI 0.95 --type CDS -S $results/MetageneAnalysis/up_trans.txt
+MetageneAnalysis -f ../data/attributes.txt -c ../results/Ref/longest.transcripts.info.txt -o $results/MetageneAnalysis/test_down_CDS_normed -U codon -M RPKM -u 0 -d 500 -l 100 -n 5 -m 1 -e 5 --norm yes -y 100 --CI 0.95 --type CDS -S $results/MetageneAnalysis/down_trans.txt
+MetageneAnalysis -f ../data/attributes.txt -c ../results/Ref/longest.transcripts.info.txt -o $results/MetageneAnalysis/test_unblocked_CDS_normed -U codon -M RPKM -u 0 -d 500 -l 100 -n 5 -m 1 -e 5 --norm yes -y 100 --CI 0.95 --type CDS -S $results/MetageneAnalysis/unblocked_trans.txt
+
+Rscript GetCommonGeneSets.R
diff --git a/RuningTimeTest/Fly/code/QC.sh b/RuningTimeTest/Fly/code/QC.sh
@@ -0,0 +1,54 @@
+#########################################################################
+# File Name: QC.sh
+# Author: lifj
+# mail: [email protected]
+# Created Time: Tue 09 Jun 2020 02:47:28 PM CST
+#########################################################################
+#!/bin/bash
+#BSUB -J QC.sh
+#BSUB -o QC.out
+#BSUB -e QC.err
+#BSUB -n 1
+#BSUB -q TEST-A
+
+
+
+## periodicity
+results=../results
+mkdir -p $results/periodicity
+cd $results/periodicity
+i=SRR3297803
+Periodicity -a ../../results/Ref/RiboCode_annot -i ../../data/00.STAR/${i}_STAR/$i.Aligned.toTranscriptome.out.sorted.bam -o test_${i} -c ../../results/Ref/longest.transcripts.info.txt -L 25 -R 35
+cd ../../code
+echo "periodicity finished!"
+
+## length
+mkdir -p $results/length
+cd $results/length
+i=SRR3297803
+LengthDistribution -i ../../data/00.STAR/${i}_STAR/${i}.Aligned.sortedByCoord.out.bam -o test_$i -f bam
+cd ../../code
+echo "length finished!"
+
+## RPF statistics
+mkdir -p $results/RPF_statisitcs
+cd $results/RPF_statisitcs
+i=SRR3297803
+StatisticReadsOnDNAsContam -i ../../data/00.STAR/${i}_STAR/${i}.Aligned.sortedByCoord.out.bam -g ../../results/Ref/Drosophila_melanogaster.BDGP6.22.98.gtf -o test_${i}
+cd ../../code
+echo "RPF statistics finished!"
+
+## RiboDensityOfDiffFrames
+mkdir -p $results/RiboDensityFromDiffFrames
+RiboDensityOfDiffFrames -f ../data/attributes.txt -c ../results/Ref/longest.transcripts.info.txt -o $results/RiboDensityFromDiffFrames/test --plot yes
+echo "RiboDensityFromDiffFrames.sh finished!"
+
+
+#bash periodicity.sh
+#echo "periodicity.sh finished!"
+#bash length.sh
+#echo "length.sh finished!"
+#bash RPF_statistics.sh
+#echo "RPF_statisitcs.sh finished!"
+#bash RiboDensityFromDiffFrames.sh
+#echo "RiboDensityFromDiffFrames.sh finished!"
diff --git a/RuningTimeTest/Fly/code/fileTransfer.sh b/RuningTimeTest/Fly/code/fileTransfer.sh
@@ -0,0 +1,27 @@
+#########################################################################
+# File Name: fileTransfer.sh
+# Author: lifj
+# mail: [email protected]
+# Created Time: Tue 09 Jun 2020 10:08:02 PM CST
+#########################################################################
+#!/bin/bash
+#BSUB -J fileTransfer.sh
+#BSUB -o %J.out
+#BSUB -e %J.err
+#BSUB -n 4
+#BSUB -q TEST-A
+
+mkdir -p ../results/output
+
+cp ../results/periodicity/test_SRR3297803*.pdf ../results/output
+cp ../results/length/test_SRR3297803_reads_length.pdf ../results/output
+cp ../results/RPF_statisitcs/* ../results/output
+cp ../results/RiboDensityFromDiffFrames/test_Low-detergent-2_reading_frames.pdf ../results/output
+cp ../results/MetageneAnalysis/test_whole_mean_metaplot.pdf ../results/MetageneAnalysis/test_mean_polarity.pdf ../results/output
+cp ../results/MetageneAnalysis/test_CDS_normed_mean_start*.pdf ../results/MetageneAnalysis/test_CDS_normed_mean_stop*.pdf ../results/output
+cp ../results/MetageneAnalysis/test_UTR_normed_mean_start*.pdf ../results/MetageneAnalysis/test_UTR_normed_mean_stop*.pdf ../results/output
+cp ../results/FeatureAnalysis/up_density_on_each_kind_of*.pdf ../results/output
+cp ../results/FeatureAnalysis/up*.pdf ../results/output
+cp ../results/FeatureAnalysis/test*_average_*.pdf ../results/output
+
+echo "files transfered finished!"