scripts/Pcitri_map_Illumina_to_IsoSeq_commands.txt Version 1
_p_SUSPHIRE/_I_T31_mealybug/_S_P4_Pcitri_IsoSeq/_A_04_mapIllumina-STAR/
SEEK ID: https://fairdomhub.org/data_files/5924?version=1
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scripts/Pcitri_map_Illumina_to_IsoSeq_commands.txt
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# mapping P. citri SUSPHIRE Illumina reads to IsoSeq using STAR mkdir /DATB/markop/_S_P4_Pcitri_IsoSeq/_A_04_mapIllumina-STAR/ mkdir /DATB/markop/_S_P4_Pcitri_IsoSeq/_A_04_mapIllumina-STAR/scripts mkdir /DATB/markop/_S_P4_Pcitri_IsoSeq/_A_04_mapIllumina-STAR/output mkdir /DATB/markop/_S_P4_Pcitri_IsoSeq/_A_04_mapIllumina-STAR/input/ mkdir /DATB/markop/_S_P4_Pcitri_IsoSeq/_A_04_mapIllumina-STAR/input/star_index cd /DATB/markop/_S_P4_Pcitri_IsoSeq/_A_04_mapIllumina-STAR/scripts #create non-redundant IsoSeq fasta cat ../../_A_02_cDNAcupcake-dry/output/Pcitri.collapsed.filtered.rep.fa ../../_A_02_cDNAcupcake-dry/output/Pcitri.ignored_ids.fasta > ../input/Pcitri.IsoSeq_nonred.fasta conda activate mpe_rnaseq # use IsoSeq (non-redundant) as reference for mapping STAR --runThreadN 30 --runMode genomeGenerate \ --genomeDir ../input/star_index \ --genomeFastaFiles ../input/Pcitri.IsoSeq_nonred.fasta \ --limitGenomeGenerateRAM=220000000000 #you cannot have paired and single end reads in same mapping!!! #also with multiple PE samples separated with comma I get a Segmentation fault error :( will do each sample separately ##mapping only paired reads #ulimit default 1024 ulimit -n 10000 #load genome STAR --genomeLoad LoadAndExit --genomeDir ../input/star_index #SUSPHIRE_VF1 STAR \ --runMode alignReads \ --runThreadN 32 \ --genomeDir ../input/star_index \ --readFilesIn \ /NFSs-datarepo/ngs_omics/NGS_pci_rna-seq_2018_mpe_Pcitri/data/VF_02_1.fastq.gz \ /NFSs-datarepo/ngs_omics/NGS_pci_rna-seq_2018_mpe_Pcitri/data/VF_02_2.fastq.gz \ --outFileNamePrefix ../output/Pcitri_mapToIsoSeq_STAR_SVF02_ \ --outSAMtype BAM SortedByCoordinate \ --readFilesCommand pigz -c -d #SUSPHIRE_VF2 STAR \ --runMode alignReads \ --runThreadN 32 \ --genomeDir ../input/star_index \ --readFilesIn \ /NFSs-datarepo/ngs_omics/NGS_pci_rna-seq_2018_mpe_Pcitri/data/VF_03_1.fastq.gz \ /NFSs-datarepo/ngs_omics/NGS_pci_rna-seq_2018_mpe_Pcitri/data/VF_03_2.fastq.gz \ --outFileNamePrefix ../output/Pcitri_mapToIsoSeq_STAR_SVF03_ \ --outSAMtype BAM SortedByCoordinate \ --readFilesCommand pigz -c -d #SUSPHIRE_VF3 STAR \ --runMode alignReads \ --runThreadN 32 \ --genomeDir ../input/star_index \ --readFilesIn \ /NFSs-datarepo/ngs_omics/NGS_pci_rna-seq_2018_mpe_Pcitri/data/VF_05_1.fastq.gz \ /NFSs-datarepo/ngs_omics/NGS_pci_rna-seq_2018_mpe_Pcitri/data/VF_05_2.fastq.gz \ --outFileNamePrefix ../output/Pcitri_mapToIsoSeq_STAR_SVF05_ \ --outSAMtype BAM SortedByCoordinate \ --readFilesCommand pigz -c -d #SUSPHIRE_VF4 STAR \ --runMode alignReads \ --runThreadN 32 \ --genomeDir ../input/star_index \ --readFilesIn \ /NFSs-datarepo/ngs_omics/NGS_pci_rna-seq_2018_mpe_Pcitri/data/VF_06_1.fastq.gz \ /NFSs-datarepo/ngs_omics/NGS_pci_rna-seq_2018_mpe_Pcitri/data/VF_06_2.fastq.gz \ --outFileNamePrefix ../output/Pcitri_mapToIsoSeq_STAR_SVF06_ \ --outSAMtype BAM SortedByCoordinate \ --readFilesCommand pigz -c -d #SUSPHIRE_MF1 STAR \ --runMode alignReads \ --runThreadN 32 \ --genomeDir ../input/star_index \ --readFilesIn \ /NFSs-datarepo/ngs_omics/NGS_pci_rna-seq_2018_mpe_Pcitri/data/MF_08_1.fastq.gz \ /NFSs-datarepo/ngs_omics/NGS_pci_rna-seq_2018_mpe_Pcitri/data/MF_08_2.fastq.gz \ --outFileNamePrefix ../output/Pcitri_mapToIsoSeq_STAR_SMF08_ \ --outSAMtype BAM SortedByCoordinate \ --readFilesCommand pigz -c -d #SUSPHIRE_MF2 STAR \ --runMode alignReads \ --runThreadN 32 \ --genomeDir ../input/star_index \ --readFilesIn \ /NFSs-datarepo/ngs_omics/NGS_pci_rna-seq_2018_mpe_Pcitri/data/MF_09_1.fastq.gz \ /NFSs-datarepo/ngs_omics/NGS_pci_rna-seq_2018_mpe_Pcitri/data/MF_09_2.fastq.gz \ --outFileNamePrefix ../output/Pcitri_mapToIsoSeq_STAR_SMF09_ \ --outSAMtype BAM SortedByCoordinate \ --readFilesCommand pigz -c -d #SUSPHIRE_MF3 STAR \ --runMode alignReads \ --runThreadN 32 \ --genomeDir ../input/star_index \ --readFilesIn \ /NFSs-datarepo/ngs_omics/NGS_pci_rna-seq_2018_mpe_Pcitri/data/MF_10_1.fastq.gz \ /NFSs-datarepo/ngs_omics/NGS_pci_rna-seq_2018_mpe_Pcitri/data/MF_10_2.fastq.gz \ --outFileNamePrefix ../output/Pcitri_mapToIsoSeq_STAR_SMF10_ \ --outSAMtype BAM SortedByCoordinate \ --readFilesCommand pigz -c -d #SUSPHIRE_MF4 STAR \ --runMode alignReads \ --runThreadN 32 \ --genomeDir ../input/star_index \ --readFilesIn \ /NFSs-datarepo/ngs_omics/NGS_pci_rna-seq_2018_mpe_Pcitri/data/MF_11_1.fastq.gz \ /NFSs-datarepo/ngs_omics/NGS_pci_rna-seq_2018_mpe_Pcitri/data/MF_11_2.fastq.gz \ --outFileNamePrefix ../output/Pcitri_mapToIsoSeq_STAR_SMF11_ \ --outSAMtype BAM SortedByCoordinate \ --readFilesCommand pigz -c -d #*** #Edinburgh_ALL1 STAR \ --runMode alignReads \ --runThreadN 32 \ --genomeDir ../input/star_index \ --readFilesIn \ /NFSs-datarepo/ngs_omics/NGS_pci_rna-seq_2019_mpe_SUSPHIRE-Edinburgh/data/PC_ALL_1_1.fastq.gz \ /NFSs-datarepo/ngs_omics/NGS_pci_rna-seq_2019_mpe_SUSPHIRE-Edinburgh/data/PC_ALL_1_2.fastq.gz \ --outFileNamePrefix ../output/Pcitri_mapToIsoSeq_STAR_EALL1_ \ --outSAMtype BAM SortedByCoordinate \ --readFilesCommand pigz -c -d #Edinburgh_F1 STAR \ --runMode alignReads \ --runThreadN 6 \ --genomeDir ../input/star_index \ --readFilesIn \ /NFSs-datarepo/ngs_omics/NGS_pci_rna-seq_2019_mpe_SUSPHIRE-Edinburgh/data/PC_F_1_1.fastq.gz \ /NFSs-datarepo/ngs_omics/NGS_pci_rna-seq_2019_mpe_SUSPHIRE-Edinburgh/data/PC_F_1_2.fastq.gz \ --outFileNamePrefix ../output/Pcitri_mapToIsoSeq_STAR_EF1_ \ --outSAMtype BAM SortedByCoordinate \ --readFilesCommand pigz -c -d #Edinburgh_F2 STAR \ --runMode alignReads \ --runThreadN 32 \ --genomeDir ../input/star_index \ --readFilesIn \ /NFSs-datarepo/ngs_omics/NGS_pci_rna-seq_2019_mpe_SUSPHIRE-Edinburgh/data/PC_F_2_1.fastq.gz \ /NFSs-datarepo/ngs_omics/NGS_pci_rna-seq_2019_mpe_SUSPHIRE-Edinburgh/data/PC_F_2_2.fastq.gz \ --outFileNamePrefix ../output/Pcitri_mapToIsoSeq_STAR_EF2_ \ --outSAMtype BAM SortedByCoordinate \ --readFilesCommand pigz -c -d #Edinburgh_F3 STAR \ --runMode alignReads \ --runThreadN 32 \ --genomeDir ../input/star_index \ --readFilesIn \ /NFSs-datarepo/ngs_omics/NGS_pci_rna-seq_2019_mpe_SUSPHIRE-Edinburgh/data/PC_F_3_1.fastq.gz \ /NFSs-datarepo/ngs_omics/NGS_pci_rna-seq_2019_mpe_SUSPHIRE-Edinburgh/data/PC_F_3_2.fastq.gz \ --outFileNamePrefix ../output/Pcitri_mapToIsoSeq_STAR_EF3_ \ --outSAMtype BAM SortedByCoordinate \ --readFilesCommand pigz -c -d #Edinburgh_M1 STAR \ --runMode alignReads \ --runThreadN 32 \ --genomeDir ../input/star_index \ --readFilesIn \ /NFSs-datarepo/ngs_omics/NGS_pci_rna-seq_2019_mpe_SUSPHIRE-Edinburgh/data/PC_M_1_1.fastq.gz \ /NFSs-datarepo/ngs_omics/NGS_pci_rna-seq_2019_mpe_SUSPHIRE-Edinburgh/data/PC_M_1_2.fastq.gz \ --outFileNamePrefix ../output/Pcitri_mapToIsoSeq_STAR_EM1_ \ --outSAMtype BAM SortedByCoordinate \ --readFilesCommand pigz -c -d #Edinburgh_M2 STAR \ --runMode alignReads \ --runThreadN 32 \ --genomeDir ../input/star_index \ --readFilesIn \ /NFSs-datarepo/ngs_omics/NGS_pci_rna-seq_2019_mpe_SUSPHIRE-Edinburgh/data/PC_M_2_1.fastq.gz \ /NFSs-datarepo/ngs_omics/NGS_pci_rna-seq_2019_mpe_SUSPHIRE-Edinburgh/data/PC_M_2_2.fastq.gz \ --outFileNamePrefix ../output/Pcitri_mapToIsoSeq_STAR_EM2_ \ --outSAMtype BAM SortedByCoordinate \ --readFilesCommand pigz -c -d #Edinburgh_M3 STAR \ --runMode alignReads \ --runThreadN 32 \ --genomeDir ../input/star_index \ --readFilesIn \ /NFSs-datarepo/ngs_omics/NGS_pci_rna-seq_2019_mpe_SUSPHIRE-Edinburgh/data/PC_M_3_1.fastq.gz \ /NFSs-datarepo/ngs_omics/NGS_pci_rna-seq_2019_mpe_SUSPHIRE-Edinburgh/data/PC_M_3_2.fastq.gz \ --outFileNamePrefix ../output/Pcitri_mapToIsoSeq_STAR_EM3_ \ --outSAMtype BAM SortedByCoordinate \ --readFilesCommand pigz -c -d #unload genome STAR --genomeLoad Remove --genomeDir ../input/star_index ##### we also want to count the reads that are mapped to each transcript and perform DE analysis in R (limma-voom) #index bam files samtools index -@ 6 ../output/Pcitri_mapToIsoSeq_STAR_EALL1_Aligned.sortedByCoord.out.bam samtools index -@ 6 ../output/Pcitri_mapToIsoSeq_STAR_SMF10_Aligned.sortedByCoord.out.bam samtools index -@ 6 ../output/Pcitri_mapToIsoSeq_STAR_EM2_Aligned.sortedByCoord.out.bam samtools index -@ 6 ../output/Pcitri_mapToIsoSeq_STAR_EM1_Aligned.sortedByCoord.out.bam samtools index -@ 6 ../output/Pcitri_mapToIsoSeq_STAR_SVF05_Aligned.sortedByCoord.out.bam samtools index -@ 6 ../output/Pcitri_mapToIsoSeq_STAR_SMF09_Aligned.sortedByCoord.out.bam samtools index -@ 6 ../output/Pcitri_mapToIsoSeq_STAR_SVF06_Aligned.sortedByCoord.out.bam samtools index -@ 6 ../output/Pcitri_mapToIsoSeq_STAR_EF3_Aligned.sortedByCoord.out.bam samtools index -@ 6 ../output/Pcitri_mapToIsoSeq_STAR_EM3_Aligned.sortedByCoord.out.bam samtools index -@ 6 ../output/Pcitri_mapToIsoSeq_STAR_SVF02_Aligned.sortedByCoord.out.bam samtools index -@ 6 ../output/Pcitri_mapToIsoSeq_STAR_SMF08_Aligned.sortedByCoord.out.bam samtools index -@ 6 ../output/Pcitri_mapToIsoSeq_STAR_SMF11_Aligned.sortedByCoord.out.bam samtools index -@ 6 ../output/Pcitri_mapToIsoSeq_STAR_EF2_Aligned.sortedByCoord.out.bam samtools index -@ 6 ../output/Pcitri_mapToIsoSeq_STAR_SVF03_Aligned.sortedByCoord.out.bam samtools index -@ 6 ../output/Pcitri_mapToIsoSeq_STAR_EF1_Aligned.sortedByCoord.out.bam #### get counts with samtools idxstats samtools idxstats -@ 6 ../output/Pcitri_mapToIsoSeq_STAR_EALL1_Aligned.sortedByCoord.out.bam > ../output/Pcitri_mapToIsoSeq_STAR_EALL1.counts samtools idxstats -@ 6 ../output/Pcitri_mapToIsoSeq_STAR_SMF10_Aligned.sortedByCoord.out.bam > ../output/Pcitri_mapToIsoSeq_STAR_SMF10.counts samtools idxstats -@ 6 ../output/Pcitri_mapToIsoSeq_STAR_EM2_Aligned.sortedByCoord.out.bam > ../output/Pcitri_mapToIsoSeq_STAR_EM2.counts samtools idxstats -@ 6 ../output/Pcitri_mapToIsoSeq_STAR_EM1_Aligned.sortedByCoord.out.bam > ../output/Pcitri_mapToIsoSeq_STAR_EM1.counts samtools idxstats -@ 6 ../output/Pcitri_mapToIsoSeq_STAR_SVF05_Aligned.sortedByCoord.out.bam > ../output/Pcitri_mapToIsoSeq_STAR_SVF05.counts samtools idxstats -@ 6 ../output/Pcitri_mapToIsoSeq_STAR_SMF09_Aligned.sortedByCoord.out.bam > ../output/Pcitri_mapToIsoSeq_STAR_SMF09.counts samtools idxstats -@ 6 ../output/Pcitri_mapToIsoSeq_STAR_SVF06_Aligned.sortedByCoord.out.bam > ../output/Pcitri_mapToIsoSeq_STAR_SVF06.counts samtools idxstats -@ 6 ../output/Pcitri_mapToIsoSeq_STAR_EF3_Aligned.sortedByCoord.out.bam > ../output/Pcitri_mapToIsoSeq_STAR_EF3.counts samtools idxstats -@ 6 ../output/Pcitri_mapToIsoSeq_STAR_EM3_Aligned.sortedByCoord.out.bam > ../output/Pcitri_mapToIsoSeq_STAR_EM3.counts samtools idxstats -@ 6 ../output/Pcitri_mapToIsoSeq_STAR_SVF02_Aligned.sortedByCoord.out.bam > ../output/Pcitri_mapToIsoSeq_STAR_SVF02.counts samtools idxstats -@ 6 ../output/Pcitri_mapToIsoSeq_STAR_SMF08_Aligned.sortedByCoord.out.bam > ../output/Pcitri_mapToIsoSeq_STAR_SMF08.counts samtools idxstats -@ 6 ../output/Pcitri_mapToIsoSeq_STAR_SMF11_Aligned.sortedByCoord.out.bam > ../output/Pcitri_mapToIsoSeq_STAR_SMF11.counts samtools idxstats -@ 6 ../output/Pcitri_mapToIsoSeq_STAR_EF2_Aligned.sortedByCoord.out.bam > ../output/Pcitri_mapToIsoSeq_STAR_EF2.counts samtools idxstats -@ 6 ../output/Pcitri_mapToIsoSeq_STAR_SVF03_Aligned.sortedByCoord.out.bam > ../output/Pcitri_mapToIsoSeq_STAR_SVF03.counts samtools idxstats -@ 6 ../output/Pcitri_mapToIsoSeq_STAR_EF1_Aligned.sortedByCoord.out.bam > ../output/Pcitri_mapToIsoSeq_STAR_EF1.counts #run R to combine all counts in to an expression matrix ##############################################################################
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Created: 16th May 2022 at 11:47
Last updated: 6th Nov 2024 at 15:26
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Version 1 (earliest) Created 16th May 2022 at 11:47 by Marko Petek
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https://orcid.org/0000-0003-3644-7827PhD in Biotechnology, Research Associate at Department of Biotechnology and Systems Biology, National Institute of Biology
National Institute of Biology, Department of Biotechnology and Systems Biology projects
Projects: HYp - Spatiotemporal analysis of hypersensitive response to Potato virus Y in potato, pISA-tree, MOA - Multiomics analysis of potato response to Potato virus Y (PVY) infection, SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture, INDIE - Biotechnological production of sustainable indole, _p_stRT, ADAPT - Accelerated Development of multiple-stress tolerAnt PoTato, _p_RNAinVAL, tst, tst2, Playground
Web page: http://www.nib.si/eng/index.php/departments/department-of-biotechnology-and-systems-biology
SUSPHIRE aims to provide a sustainable, low-cost biomanufacturing platform for the commercial production of insect pheromones.
Synthetic biology data management spreadsheet: https://fairdomhub.org/data_files/6036
Programme: NIBSys
Public web page: http://susphire.info/susphireproject/
Start date: 1st Apr 2018
End date: 30th Sep 2021
Short Name: T31_mealybug Title: Mealybug genome and transcriptome analyses Description: Searching for enzymes involved in the mealybug pheromone biosynthesis pathways. These pheromones are known to be released by virgin females. Phenodata: ./phenodata_20190523.txt Featuredata: Principal investigator: Heribert Warzecha, Špela Baebler License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes
Submitter: Marko Petek
Studies: Investigation files, _S_P3_expressionEcoli, _S_P4_AdPathGenes, _S_P4_Pcitri_IsoSeq, _S_P4_Pcitri_genome, _S_P4_Pcitri_genome_extSamples, _S_P4_Pcitri_tr1, _S_P4_Pcitri_tr1tr2combo, _S_P4_Pcitri_tr2, _S_P4_cand_all, _S_P4_cand_genomic
Assays: _A_01-CoEXpNetViz_tr2-coexpr, _A_01_NGI-IsoSeq, _A_01_RNAseq-CLC, _A_01_assembly2-rnaSPAdes, _A_01_mapToGenomeAll-STAR, _A_01_renameFASTA-Bioinfo, _A_02-CoEXpNetViz_gen-coexpr, _A_02_CDHIT-Bioinfo, _A_02_assembly2-IPS, _A_02_cDNAcupcake-dry, _A_02_limma-R, _A_02_mapToGenomeAll_limma-R, _A_03-IPS, _A_03_CDHIT2-Bioinfo, _A_03_limma_min50counts-R, _A_03_mapAs2ToGenome-STAR, _A_04_limma_min10counts-R, _A_04_mapIllumina-STAR, _A_04_mapReadsToAs2-STAR, _A_05_As2_tr_limmaDE-R, _A_05_DE_limma-R, _A_05_assembly1-rnaSPAdes, _A_06_assembly1-IPS, _A_07_mapAs1ToGenome-STAR, _A_08_mapReadsToAs1-STAR, _A_09_As1_tr_limmaDE-R, _A_C98F-EcoliExpr, _A_IDIsearch-Bioinfo, _A_IPS-bioinfo, _A_MAST-bioinfo, _A_MEME-bioinfo, _A_MSA-bioinfo, _A_MeUppS-EcoliExpr, _A_Node14610-EcoliExpr, _A_Node14610DmTP-EcoliExpr, _A_OtherMealybugCandidates-Alignment, _A_Pc1599-EcoliExpr, _A_Pc23180-EcoliExpr, _A_Pc2704-EcoliExpr, _A_Pc32607-EcoliExpr, _A_Pc7366II-EcoliExpr, _A_PcCis24-EcoliExpr, _A_Strep_CLDS-bioinfo, _A_TPS_phy-bioinfo, _A_Terzyme-bioinfo, _A_Trans1153-EcoliExpr, _A_Trans2-EcoliExpr, _A_Trans39-EcoliExpr, _A_Trans57-EcoliExpr, _A_Trans64-EcoliExpr, _A_Trans94-EcoliExpr, _A_candidatemining-bioinfo, _A_g14825_recon-bioinfo, _A_smallIDSsubunit-motifs, _I_T31_mealybug-files, _S_P3_expressionEcoli-files, _S_P4_AdPathGenes-files, _S_P4_Pcitri_IsoSeq-files, _S_P4_Pcitri_genome-files, _S_P4_Pcitri_genome_extSamples-files, _S_P4_Pcitri_tr1-files, _S_P4_Pcitri_tr1tr2combo-files, _S_P4_Pcitri_tr2-files, _S_P4_cand_all-files, _S_P4_cand_genomic-files
Short Name: P4_Pcitri_IsoSeq Title: P citri Iso-Seq transcriptome generation and search for new sex pheromone biosynthesis genes Description: PacBio IsoSeq transcriptome sequencing and data analysis Raw Data: SRR15093694 Principal investigator: Špela Baebler License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes
Submitter: Marko Petek
Investigation: _I_T31_mealybug
Assays: _A_01_NGI-IsoSeq, _A_02_cDNAcupcake-dry, _A_03-IPS, _A_04_mapIllumina-STAR, _A_05_DE_limma-R, _S_P4_Pcitri_IsoSeq-files
Short Name: 04_mapIllumina-STAR Assay Class: DRY Assay Type: STAR Title: Mapping Illumina reads to P citri Iso-Seq transcriptome Description: Mapping and counting Illumina reads to P citri Iso-Seq transcriptome using STAR pISA Assay creation date: 2020-10-01 pISA Assay creator: MPE Phenodata: ../../phenodata_20190523.txt Featuredata: Data:
Submitter: Marko Petek
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: _I_T31_mealybug
Study: _S_P4_Pcitri_IsoSeq
