/work/GIF/remkv6/Baum/04_Dovetail2Restart/38_Expression/01_AllExpressionDatasetsSeparate
#/work/GIF/remkv6/Baum/04_Dovetail2Restart/39_DifferentialExpression/02_mRNA
ln -s /work/GIF/remkv6/Baum/04_Dovetail2Restart/49_RenameChromosomes/01_Transfer2Box/OrderedSCNGenePredictions.gff3
ln -s ../../49_RenameChromosomes/01_Transfer2Box/SCNgenome.fasta
#grab all the trimmed reads from the previous run on a differently named genome
for f in ../../11_AlignRNA/*val_1.fq.gz; do ln -s $f;done
for f in ../../11_AlignRNA/*val_2.fq.gz; do ln -s $f;done
#One of the samples had odd trimming and had to be left untrimmed because it would not map.
ln -s /work/GIF/remkv6/Baum/03_GlandRepeat738/00_TrimReads/1703FL-02-01_S1_L001_R2_001.fastq.gz
ln -s /work/GIF/remkv6/Baum/03_GlandRepeat738/00_TrimReads/1703FL-02-01_S1_L001_R1_001.fastq.gz
ml miniconda3; source activate RSeQC
#need to create a bed12 annotation file
#I already have bams aligned unstranded, so I used those.
for f in ../../11_AlignRNA/*bam; do echo $f; infer_experiment.py -i $f -r mikado.loci.ancestral.bed12 >${f}.Strand ;done
../../11_AlignRNA/1703FL-02-01_S1_L001_R1_001_val_1.fq_sorted.bam
This is PairEnd Data
Fraction of reads failed to determine: 0.0962
Fraction of reads explained by "1++,1--,2+-,2-+": 0.8428
Fraction of reads explained by "1+-,1-+,2++,2--": 0.0610
../../11_AlignRNA/1703FL-02-02_S2_L001_R1_001_val_1.fq_sorted.bam
This is PairEnd Data
Fraction of reads failed to determine: 0.1704
Fraction of reads explained by "1++,1--,2+-,2-+": 0.7922
Fraction of reads explained by "1+-,1-+,2++,2--": 0.0373
../../11_AlignRNA/1703FL-02-03_S3_L001_R1_001_val_1.fq_sorted.bam
This is PairEnd Data
Fraction of reads failed to determine: 0.1324
Fraction of reads explained by "1++,1--,2+-,2-+": 0.8398
Fraction of reads explained by "1+-,1-+,2++,2--": 0.0278
../../11_AlignRNA/1703FL-02-04_S4_L001_R1_001_val_1.fq_sorted.bam
This is PairEnd Data
Fraction of reads failed to determine: 0.1149
Fraction of reads explained by "1++,1--,2+-,2-+": 0.8497
Fraction of reads explained by "1+-,1-+,2++,2--": 0.0354
../../11_AlignRNA/1703-TM101_S0_L003_R1_001_val_1.fq_sorted.bam
This is PairEnd Data
Fraction of reads failed to determine: 0.0993
Fraction of reads explained by "1++,1--,2+-,2-+": 0.8351
Fraction of reads explained by "1+-,1-+,2++,2--": 0.0656
../../11_AlignRNA/1703-TM102_S0_L003_R1_001_val_1.fq_sorted.bam
This is PairEnd Data
Fraction of reads failed to determine: 0.1150
Fraction of reads explained by "1++,1--,2+-,2-+": 0.8491
Fraction of reads explained by "1+-,1-+,2++,2--": 0.0359
../../11_AlignRNA/AllRNASEQ_sorted.bam
This is PairEnd Data
Fraction of reads failed to determine: 0.2571
Fraction of reads explained by "1++,1--,2+-,2-+": 0.5031
Fraction of reads explained by "1+-,1-+,2++,2--": 0.2398
../../11_AlignRNA/SCNgenome.consensus_isoforms_sorted.bam
This is SingleEnd Data
Fraction of reads failed to determine: 0.1303
Fraction of reads explained by "++,--": 0.8118
Fraction of reads explained by "+-,-+": 0.0580
../../11_AlignRNA/SCNgenome.H.glycinesEST_sorted.bam
This is SingleEnd Data
Fraction of reads failed to determine: 0.0928
Fraction of reads explained by "++,--": 0.7269
Fraction of reads explained by "+-,-+": 0.1803
../../11_AlignRNA/SRR6230579_1_val_1.fq_sorted.bam
This is PairEnd Data
Fraction of reads failed to determine: 0.1536
Fraction of reads explained by "1++,1--,2+-,2-+": 0.8245
Fraction of reads explained by "1+-,1-+,2++,2--": 0.0220
../../11_AlignRNA/SRR6230580_1_val_1.fq_sorted.bam
This is PairEnd Data
Fraction of reads failed to determine: 0.0796
Fraction of reads explained by "1++,1--,2+-,2-+": 0.0229
Fraction of reads explained by "1+-,1-+,2++,2--": 0.8974
../../11_AlignRNA/SRR6230581_1_val_1.fq_sorted.bam
This is PairEnd Data
Fraction of reads failed to determine: 0.1618
Fraction of reads explained by "1++,1--,2+-,2-+": 0.0187
Fraction of reads explained by "1+-,1-+,2++,2--": 0.8195
../../11_AlignRNA/SRR6230582_1_val_1.fq_sorted.bam
This is PairEnd Data
Fraction of reads failed to determine: 0.1507
Fraction of reads explained by "1++,1--,2+-,2-+": 0.8252
Fraction of reads explained by "1+-,1-+,2++,2--": 0.0240
../../11_AlignRNA/SRR6230583_1_val_1.fq_sorted.bam
This is PairEnd Data
Fraction of reads failed to determine: 0.1450
Fraction of reads explained by "1++,1--,2+-,2-+": 0.8334
Fraction of reads explained by "1+-,1-+,2++,2--": 0.0216
../../11_AlignRNA/SRR6230584_1_val_1.fq_sorted.bam
This is PairEnd Data
Fraction of reads failed to determine: 0.1424
Fraction of reads explained by "1++,1--,2+-,2-+": 0.8339
Fraction of reads explained by "1+-,1-+,2++,2--": 0.0238
../../11_AlignRNA/SRR6230585_1_val_1.fq_sorted.bam
This is PairEnd Data
Fraction of reads failed to determine: 0.1442
Fraction of reads explained by "1++,1--,2+-,2-+": 0.0205
Fraction of reads explained by "1+-,1-+,2++,2--": 0.8353
../../11_AlignRNA/SRR6230586_1_val_1.fq_sorted.bam
This is PairEnd Data
Fraction of reads failed to determine: 0.1259
Fraction of reads explained by "1++,1--,2+-,2-+": 0.8562
Fraction of reads explained by "1+-,1-+,2++,2--": 0.0179
../../11_AlignRNA/SRR6230587_1_val_1.fq_sorted.bam
This is PairEnd Data
Fraction of reads failed to determine: 0.1234
Fraction of reads explained by "1++,1--,2+-,2-+": 0.8559
Fraction of reads explained by "1+-,1-+,2++,2--": 0.0206
#/work/GIF/remkv6/Baum/04_Dovetail2Restart/39_DifferentialExpression/02_mRNA
paste <(ls -1 *l_1.fq.gz) <(ls -1 *l_2.fq.gz) |while read line; do echo "sh runFeatureCountsNBigwigStrandRFmRNA.sh "$line" /work/GIF/remkv6/Baum/04_Dovetail2Restart/38_Expression/01_AllExpressionDatasetsSeparate SCNgenome.fasta OrderedSCNGenePredictions.gff3";done >>featurecounts.sh
#Ran the above script for each of the required analyses, deleted improper script/read pairs for those that required different strandedness settings from the rest of the samples
runFeatureCountsNBigwigStrandFRgeneMult.sh runFeatureCountsNBigwigStrandFRmRNA.sh runFeatureCountsNBigwigStrandRFgene.sh
runFeatureCountsNBigwigStrandFRgene.sh runFeatureCountsNBigwigStrandRFgeneMult.sh runFeatureCountsNBigwigStrandRFmRNA.sh
#runFeatureCountsNBigwigStrandFRgene.sh
################################################################################################################################
PROC=16
R1_FQ="$1"
R2_FQ="$2"
DBDIR="$3"
GENOME="$4"
GFF="$5"
#module load trimgalore
#module load py-setuptools/35.0.2-py2-hqrsjff
#trim_galore --paired ${R1_FQ} ${R2_FQ}
module load hisat2
#hisat2-build ${GENOME} ${GENOME%.*}
hisat2 -p ${PROC} --rna-strandness FR -x ${GENOME%.*} -1 ${R1_FQ} -2 ${R2_FQ} -S ${R1_FQ%.*}Gene.sam
module load samtools
samtools view --threads ${PROC} -b -o ${R1_FQ%.*}Gene.bam ${R1_FQ%.*}Gene.sam
samtools sort -o ${R1_FQ%.*}Gene_sorted.bam -T ${R1_FQ%.*}Gene_temp --threads ${PROC} ${R1_FQ%.*}Gene.bam
module load GIF2/java/1.8.0_25-b17
module load picard/2.17.0-ft5qztz
java -jar /opt/rit/spack-app/linux-rhel7-x86_64/gcc-4.8.5/picard-2.17.0-ft5qztzntoymuxiqt3b6yi6uqcmgzmds/bin/picard.jar CollectAlignmentSummaryMetrics REFERENCE_SEQUENCE=${DBDIR}/${GENOME} INPUT=${R1_FQ%.*}Gene_sorted.bam OUTPUT=${R1_FQ%.*}Gene.bam_alignment.stats
module load subread
featureCounts -T ${PROC} -M -t gene -s 1 -g ID -a ${GFF} -o ${R1_FQ%.*}Gene_counts_genes.txt ${R1_FQ%.*}Gene_sorted.bam
module load bedtools2
bedtools genomecov -ibam ${R1_FQ%.*}Gene_sorted.bam -bga -g ${GENOME} >${R1_FQ%.*}Gene_sorted.bam.bdg
#module load bioawk
#bioawk -c fastx '{print $name,length($seq)}' ${GENOME} >Chr.sizes
/home/remkv6/common_scripts/kentUtils/bin/linux.x86_64/bedGraphToBigWig ${R1_FQ%.*}Gene_sorted.bam.bdg Chr.sizes ${R1_FQ%.*}Gene_sorted.bw
#######################################################################################################################
#the resulting scripts that were Ran
#featurecounts.sh
#########################################################################################################################
sh runFeatureCountsNBigwigStrandFRgeneMult.sh 1703FL-02-01_S1_L001_R1_001_val_1.fq.gz 1703FL-02-01_S1_L001_R2_001_val_2.fq.gz /work/GIF/remkv6/Baum/04_Dovetail2Restart/38_Expression/01_AllExpressionDatasetsSeparate SCNgenome.fasta OrderedSCNGenePredictions.gff3
sh runFeatureCountsNBigwigStrandFRgeneMult.sh 1703FL-02-02_S2_L001_R1_001_val_1.fq.gz 1703FL-02-02_S2_L001_R2_001_val_2.fq.gz /work/GIF/remkv6/Baum/04_Dovetail2Restart/38_Expression/01_AllExpressionDatasetsSeparate SCNgenome.fasta OrderedSCNGenePredictions.gff3
sh runFeatureCountsNBigwigStrandFRgeneMult.sh 1703FL-02-03_S3_L001_R1_001_val_1.fq.gz 1703FL-02-03_S3_L001_R2_001_val_2.fq.gz /work/GIF/remkv6/Baum/04_Dovetail2Restart/38_Expression/01_AllExpressionDatasetsSeparate SCNgenome.fasta OrderedSCNGenePredictions.gff3
sh runFeatureCountsNBigwigStrandFRgeneMult.sh 1703FL-02-04_S4_L001_R1_001_val_1.fq.gz 1703FL-02-04_S4_L001_R2_001_val_2.fq.gz /work/GIF/remkv6/Baum/04_Dovetail2Restart/38_Expression/01_AllExpressionDatasetsSeparate SCNgenome.fasta OrderedSCNGenePredictions.gff3
sh runFeatureCountsNBigwigStrandFRgeneMult.sh 1703-TM101_S0_L003_R1_001_val_1.fq.gz 1703-TM101_S0_L003_R2_001_val_2.fq.gz /work/GIF/remkv6/Baum/04_Dovetail2Restart/38_Expression/01_AllExpressionDatasetsSeparate SCNgenome.fasta OrderedSCNGenePredictions.gff3
sh runFeatureCountsNBigwigStrandFRgeneMult.sh 1703-TM102_S0_L003_R1_001_val_1.fq.gz 1703-TM102_S0_L003_R2_001_val_2.fq.gz /work/GIF/remkv6/Baum/04_Dovetail2Restart/38_Expression/01_AllExpressionDatasetsSeparate SCNgenome.fasta OrderedSCNGenePredictions.gff3
sh runFeatureCountsNBigwigStrandFRgeneMult.sh SRR6230579_1_val_1.fq.gz SRR6230579_2_val_2.fq.gz /work/GIF/remkv6/Baum/04_Dovetail2Restart/38_Expression/01_AllExpressionDatasetsSeparate SCNgenome.fasta OrderedSCNGenePredictions.gff3
sh runFeatureCountsNBigwigStrandFRgeneMult.sh SRR6230582_1_val_1.fq.gz SRR6230582_2_val_2.fq.gz /work/GIF/remkv6/Baum/04_Dovetail2Restart/38_Expression/01_AllExpressionDatasetsSeparate SCNgenome.fasta OrderedSCNGenePredictions.gff3
sh runFeatureCountsNBigwigStrandFRgeneMult.sh SRR6230583_1_val_1.fq.gz SRR6230583_2_val_2.fq.gz /work/GIF/remkv6/Baum/04_Dovetail2Restart/38_Expression/01_AllExpressionDatasetsSeparate SCNgenome.fasta OrderedSCNGenePredictions.gff3
sh runFeatureCountsNBigwigStrandFRgeneMult.sh SRR6230584_1_val_1.fq.gz SRR6230584_2_val_2.fq.gz /work/GIF/remkv6/Baum/04_Dovetail2Restart/38_Expression/01_AllExpressionDatasetsSeparate SCNgenome.fasta OrderedSCNGenePredictions.gff3
sh runFeatureCountsNBigwigStrandFRgeneMult.sh SRR6230586_1_val_1.fq.gz SRR6230586_2_val_2.fq.gz /work/GIF/remkv6/Baum/04_Dovetail2Restart/38_Expression/01_AllExpressionDatasetsSeparate SCNgenome.fasta OrderedSCNGenePredictions.gff3
sh runFeatureCountsNBigwigStrandFRgeneMult.sh SRR6230587_1_val_1.fq.gz SRR6230587_2_val_2.fq.gz /work/GIF/remkv6/Baum/04_Dovetail2Restart/38_Expression/01_AllExpressionDatasetsSeparate SCNgenome.fasta OrderedSCNGenePredictions.gff3
sh runFeatureCountsNBigwigStrandRFgeneMult.sh SRR6230580_1_val_1.fq.gz SRR6230580_2_val_2.fq.gz /work/GIF/remkv6/Baum/04_Dovetail2Restart/38_Expression/01_AllExpressionDatasetsSeparate SCNgenome.fasta OrderedSCNGenePredictions.gff3
sh runFeatureCountsNBigwigStrandRFgeneMult.sh SRR6230581_1_val_1.fq.gz SRR6230581_2_val_2.fq.gz /work/GIF/remkv6/Baum/04_Dovetail2Restart/38_Expression/01_AllExpressionDatasetsSeparate SCNgenome.fasta OrderedSCNGenePredictions.gff3
sh runFeatureCountsNBigwigStrandRFgeneMult.sh SRR6230585_1_val_1.fq.gz SRR6230585_2_val_2.fq.gz /work/GIF/remkv6/Baum/04_Dovetail2Restart/38_Expression/01_AllExpressionDatasetsSeparate SCNgenome.fasta OrderedSCNGenePredictions.gff3
sh runFeatureCountsNBigwigStrandFRgene.sh 1703FL-02-01_S1_L001_R1_001_val_1.fq.gz 1703FL-02-01_S1_L001_R2_001_val_2.fq.gz /work/GIF/remkv6/Baum/04_Dovetail2Restart/38_Expression/01_AllExpressionDatasetsSeparate SCNgenome.fasta OrderedSCNGenePredictions.gff3
sh runFeatureCountsNBigwigStrandFRgene.sh 1703FL-02-02_S2_L001_R1_001_val_1.fq.gz 1703FL-02-02_S2_L001_R2_001_val_2.fq.gz /work/GIF/remkv6/Baum/04_Dovetail2Restart/38_Expression/01_AllExpressionDatasetsSeparate SCNgenome.fasta OrderedSCNGenePredictions.gff3
sh runFeatureCountsNBigwigStrandFRgene.sh 1703FL-02-03_S3_L001_R1_001_val_1.fq.gz 1703FL-02-03_S3_L001_R2_001_val_2.fq.gz /work/GIF/remkv6/Baum/04_Dovetail2Restart/38_Expression/01_AllExpressionDatasetsSeparate SCNgenome.fasta OrderedSCNGenePredictions.gff3
sh runFeatureCountsNBigwigStrandFRgene.sh 1703FL-02-04_S4_L001_R1_001_val_1.fq.gz 1703FL-02-04_S4_L001_R2_001_val_2.fq.gz /work/GIF/remkv6/Baum/04_Dovetail2Restart/38_Expression/01_AllExpressionDatasetsSeparate SCNgenome.fasta OrderedSCNGenePredictions.gff3
sh runFeatureCountsNBigwigStrandFRgene.sh 1703-TM101_S0_L003_R1_001_val_1.fq.gz 1703-TM101_S0_L003_R2_001_val_2.fq.gz /work/GIF/remkv6/Baum/04_Dovetail2Restart/38_Expression/01_AllExpressionDatasetsSeparate SCNgenome.fasta OrderedSCNGenePredictions.gff3
sh runFeatureCountsNBigwigStrandFRgene.sh 1703-TM102_S0_L003_R1_001_val_1.fq.gz 1703-TM102_S0_L003_R2_001_val_2.fq.gz /work/GIF/remkv6/Baum/04_Dovetail2Restart/38_Expression/01_AllExpressionDatasetsSeparate SCNgenome.fasta OrderedSCNGenePredictions.gff3
sh runFeatureCountsNBigwigStrandFRgene.sh SRR6230579_1_val_1.fq.gz SRR6230579_2_val_2.fq.gz /work/GIF/remkv6/Baum/04_Dovetail2Restart/38_Expression/01_AllExpressionDatasetsSeparate SCNgenome.fasta OrderedSCNGenePredictions.gff3
sh runFeatureCountsNBigwigStrandFRgene.sh SRR6230582_1_val_1.fq.gz SRR6230582_2_val_2.fq.gz /work/GIF/remkv6/Baum/04_Dovetail2Restart/38_Expression/01_AllExpressionDatasetsSeparate SCNgenome.fasta OrderedSCNGenePredictions.gff3
sh runFeatureCountsNBigwigStrandFRgene.sh SRR6230583_1_val_1.fq.gz SRR6230583_2_val_2.fq.gz /work/GIF/remkv6/Baum/04_Dovetail2Restart/38_Expression/01_AllExpressionDatasetsSeparate SCNgenome.fasta OrderedSCNGenePredictions.gff3
sh runFeatureCountsNBigwigStrandFRgene.sh SRR6230584_1_val_1.fq.gz SRR6230584_2_val_2.fq.gz /work/GIF/remkv6/Baum/04_Dovetail2Restart/38_Expression/01_AllExpressionDatasetsSeparate SCNgenome.fasta OrderedSCNGenePredictions.gff3
sh runFeatureCountsNBigwigStrandFRgene.sh SRR6230586_1_val_1.fq.gz SRR6230586_2_val_2.fq.gz /work/GIF/remkv6/Baum/04_Dovetail2Restart/38_Expression/01_AllExpressionDatasetsSeparate SCNgenome.fasta OrderedSCNGenePredictions.gff3
sh runFeatureCountsNBigwigStrandFRgene.sh SRR6230587_1_val_1.fq.gz SRR6230587_2_val_2.fq.gz /work/GIF/remkv6/Baum/04_Dovetail2Restart/38_Expression/01_AllExpressionDatasetsSeparate SCNgenome.fasta OrderedSCNGenePredictions.gff3
sh runFeatureCountsNBigwigStrandRFgene.sh SRR6230580_1_val_1.fq.gz SRR6230580_2_val_2.fq.gz /work/GIF/remkv6/Baum/04_Dovetail2Restart/38_Expression/01_AllExpressionDatasetsSeparate SCNgenome.fasta OrderedSCNGenePredictions.gff3
sh runFeatureCountsNBigwigStrandRFgene.sh SRR6230581_1_val_1.fq.gz SRR6230581_2_val_2.fq.gz /work/GIF/remkv6/Baum/04_Dovetail2Restart/38_Expression/01_AllExpressionDatasetsSeparate SCNgenome.fasta OrderedSCNGenePredictions.gff3
sh runFeatureCountsNBigwigStrandRFgene.sh SRR6230585_1_val_1.fq.gz SRR6230585_2_val_2.fq.gz /work/GIF/remkv6/Baum/04_Dovetail2Restart/38_Expression/01_AllExpressionDatasetsSeparate SCNgenome.fasta OrderedSCNGenePredictions.gff3
sh runFeatureCountsNBigwigStrandFRmRNA.sh 1703FL-02-01_S1_L001_R1_001_val_1.fq.gz 1703FL-02-01_S1_L001_R2_001_val_2.fq.gz /work/GIF/remkv6/Baum/04_Dovetail2Restart/38_Expression/01_AllExpressionDatasetsSeparate SCNgenome.fasta OrderedSCNGenePredictions.gff3
sh runFeatureCountsNBigwigStrandFRmRNA.sh 1703FL-02-02_S2_L001_R1_001_val_1.fq.gz 1703FL-02-02_S2_L001_R2_001_val_2.fq.gz /work/GIF/remkv6/Baum/04_Dovetail2Restart/38_Expression/01_AllExpressionDatasetsSeparate SCNgenome.fasta OrderedSCNGenePredictions.gff3
sh runFeatureCountsNBigwigStrandFRmRNA.sh 1703FL-02-03_S3_L001_R1_001_val_1.fq.gz 1703FL-02-03_S3_L001_R2_001_val_2.fq.gz /work/GIF/remkv6/Baum/04_Dovetail2Restart/38_Expression/01_AllExpressionDatasetsSeparate SCNgenome.fasta OrderedSCNGenePredictions.gff3
sh runFeatureCountsNBigwigStrandFRmRNA.sh 1703FL-02-04_S4_L001_R1_001_val_1.fq.gz 1703FL-02-04_S4_L001_R2_001_val_2.fq.gz /work/GIF/remkv6/Baum/04_Dovetail2Restart/38_Expression/01_AllExpressionDatasetsSeparate SCNgenome.fasta OrderedSCNGenePredictions.gff3
sh runFeatureCountsNBigwigStrandFRmRNA.sh 1703-TM101_S0_L003_R1_001_val_1.fq.gz 1703-TM101_S0_L003_R2_001_val_2.fq.gz /work/GIF/remkv6/Baum/04_Dovetail2Restart/38_Expression/01_AllExpressionDatasetsSeparate SCNgenome.fasta OrderedSCNGenePredictions.gff3
sh runFeatureCountsNBigwigStrandFRmRNA.sh 1703-TM102_S0_L003_R1_001_val_1.fq.gz 1703-TM102_S0_L003_R2_001_val_2.fq.gz /work/GIF/remkv6/Baum/04_Dovetail2Restart/38_Expression/01_AllExpressionDatasetsSeparate SCNgenome.fasta OrderedSCNGenePredictions.gff3
sh runFeatureCountsNBigwigStrandFRmRNA.sh SRR6230579_1_val_1.fq.gz SRR6230579_2_val_2.fq.gz /work/GIF/remkv6/Baum/04_Dovetail2Restart/38_Expression/01_AllExpressionDatasetsSeparate SCNgenome.fasta OrderedSCNGenePredictions.gff3
sh runFeatureCountsNBigwigStrandFRmRNA.sh SRR6230582_1_val_1.fq.gz SRR6230582_2_val_2.fq.gz /work/GIF/remkv6/Baum/04_Dovetail2Restart/38_Expression/01_AllExpressionDatasetsSeparate SCNgenome.fasta OrderedSCNGenePredictions.gff3
sh runFeatureCountsNBigwigStrandFRmRNA.sh SRR6230583_1_val_1.fq.gz SRR6230583_2_val_2.fq.gz /work/GIF/remkv6/Baum/04_Dovetail2Restart/38_Expression/01_AllExpressionDatasetsSeparate SCNgenome.fasta OrderedSCNGenePredictions.gff3
sh runFeatureCountsNBigwigStrandFRmRNA.sh SRR6230584_1_val_1.fq.gz SRR6230584_2_val_2.fq.gz /work/GIF/remkv6/Baum/04_Dovetail2Restart/38_Expression/01_AllExpressionDatasetsSeparate SCNgenome.fasta OrderedSCNGenePredictions.gff3
sh runFeatureCountsNBigwigStrandFRmRNA.sh SRR6230586_1_val_1.fq.gz SRR6230586_2_val_2.fq.gz /work/GIF/remkv6/Baum/04_Dovetail2Restart/38_Expression/01_AllExpressionDatasetsSeparate SCNgenome.fasta OrderedSCNGenePredictions.gff3
sh runFeatureCountsNBigwigStrandFRmRNA.sh SRR6230587_1_val_1.fq.gz SRR6230587_2_val_2.fq.gz /work/GIF/remkv6/Baum/04_Dovetail2Restart/38_Expression/01_AllExpressionDatasetsSeparate SCNgenome.fasta OrderedSCNGenePredictions.gff3
sh runFeatureCountsNBigwigStrandRFmRNA.sh SRR6230580_1_val_1.fq.gz SRR6230580_2_val_2.fq.gz /work/GIF/remkv6/Baum/04_Dovetail2Restart/38_Expression/01_AllExpressionDatasetsSeparate SCNgenome.fasta OrderedSCNGenePredictions.gff3
sh runFeatureCountsNBigwigStrandRFmRNA.sh SRR6230581_1_val_1.fq.gz SRR6230581_2_val_2.fq.gz /work/GIF/remkv6/Baum/04_Dovetail2Restart/38_Expression/01_AllExpressionDatasetsSeparate SCNgenome.fasta OrderedSCNGenePredictions.gff3
sh runFeatureCountsNBigwigStrandRFmRNA.sh SRR6230585_1_val_1.fq.gz SRR6230585_2_val_2.fq.gz /work/GIF/remkv6/Baum/04_Dovetail2Restart/38_Expression/01_AllExpressionDatasetsSeparate SCNgenome.fasta OrderedSCNGenePredictions.gff3
#########################################################################################################################
paste <(ls -1 *stats) <(cat *stats |awk '$1=="PAIR" {print $7}' ) |less
1703FL-02-01_S1_L001_R1_001.fastqGene.bam_alignment.stats 0.756435
1703FL-02-01_S1_L001_R1_001.fastqmRNA.bam_alignment.stats 0.756435
1703FL-02-01_S1_L001_R1_001.fastqMult.bam_alignment.stats 0.756435
1703FL-02-02_S2_L001_R1_001_val_1.fqGene.bam_alignment.stats 0.893617
1703FL-02-02_S2_L001_R1_001_val_1.fqmRNA.bam_alignment.stats 0.893617
1703FL-02-02_S2_L001_R1_001_val_1.fqMult.bam_alignment.stats 0.893617
1703FL-02-03_S3_L001_R1_001_val_1.fqGene.bam_alignment.stats 0.9458
1703FL-02-03_S3_L001_R1_001_val_1.fqmRNA.bam_alignment.stats 0.9458
1703FL-02-03_S3_L001_R1_001_val_1.fqMult.bam_alignment.stats 0.9458
1703FL-02-04_S4_L001_R1_001_val_1.fqGene.bam_alignment.stats 0.95839
1703FL-02-04_S4_L001_R1_001_val_1.fqmRNA.bam_alignment.stats 0.95839
1703FL-02-04_S4_L001_R1_001_val_1.fqMult.bam_alignment.stats 0.95839
1703-TM101_S0_L003_R1_001_val_1.fqGene.bam_alignment.stats 0.952391
1703-TM101_S0_L003_R1_001_val_1.fqmRNA.bam_alignment.stats 0.952391
1703-TM101_S0_L003_R1_001_val_1.fqMult.bam_alignment.stats 0.952391
1703-TM102_S0_L003_R1_001_val_1.fqGene.bam_alignment.stats 0.924849
1703-TM102_S0_L003_R1_001_val_1.fqmRNA.bam_alignment.stats 0.924849
1703-TM102_S0_L003_R1_001_val_1.fqMult.bam_alignment.stats 0.924849
SRR6230579_1_val_1.fqGene.bam_alignment.stats 0.933199
SRR6230579_1_val_1.fqmRNA.bam_alignment.stats 0.933199
SRR6230579_1_val_1.fqMult.bam_alignment.stats 0.933199
SRR6230580_1_val_1.fqGene.bam_alignment.stats 0.936017
SRR6230580_1_val_1.fqmRNA.bam_alignment.stats 0.936017
SRR6230580_1_val_1.fqMult.bam_alignment.stats 0.936017
SRR6230581_1_val_1.fqGene.bam_alignment.stats 0.949976
SRR6230581_1_val_1.fqmRNA.bam_alignment.stats 0.949976
SRR6230581_1_val_1.fqMult.bam_alignment.stats 0.949976
SRR6230582_1_val_1.fqGene.bam_alignment.stats 0.951359
SRR6230582_1_val_1.fqmRNA.bam_alignment.stats 0.951359
SRR6230582_1_val_1.fqMult.bam_alignment.stats 0.951359
SRR6230583_1_val_1.fqGene.bam_alignment.stats 0.955742
SRR6230583_1_val_1.fqmRNA.bam_alignment.stats 0.955742
SRR6230583_1_val_1.fqMult.bam_alignment.stats 0.955742
SRR6230584_1_val_1.fqGene.bam_alignment.stats 0.95413
SRR6230584_1_val_1.fqmRNA.bam_alignment.stats 0.95413
SRR6230584_1_val_1.fqMult.bam_alignment.stats 0.95413
SRR6230585_1_val_1.fqGene.bam_alignment.stats 0.949704
SRR6230585_1_val_1.fqmRNA.bam_alignment.stats 0.949704
SRR6230585_1_val_1.fqMult.bam_alignment.stats 0.949704
SRR6230586_1_val_1.fqGene.bam_alignment.stats 0.941641
SRR6230586_1_val_1.fqmRNA.bam_alignment.stats 0.941641
SRR6230586_1_val_1.fqMult.bam_alignment.stats 0.941641
SRR6230587_1_val_1.fqGene.bam_alignment.stats 0.956628
SRR6230587_1_val_1.fqmRNA.bam_alignment.stats 0.956628
SRR6230587_1_val_1.fqMult.bam_alignment.stats 0.956628