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RNA-Seq differential expression
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| bowtie2-build dmel-all-chromosome-r6.03.fasta dmel.bowtie.index | |
| ln -s dmel-all-chromosome-r6.03.fasta dmel.bowtie.index.fa | |
| tophat2 -p 4 --GTF dmel-all-r6.03.gff --transcriptome-index dmel.transcriptome.tophat dmel.bowtie.index | |
| tophat2 -p 4 --no-novel-juncs --GTF dmel-all-r6.03.gff --transcriptome-index dmel.transcriptome.tophat -o 3_TTAGGC_L003_R1_001.tophat dmel.bowtie.index 3_TTAGGC_L003_R1_001.fastq.gz | |
| tophat2 -p 4 --no-novel-juncs --GTF dmel-all-r6.03.gff --transcriptome-index dmel.transcriptome.tophat -o 4_TGACCA_L003_R1_001.tophat dmel.bowtie.index 4_TGACCA_L003_R1_001.fastq.gz | |
| tophat2 -p 4 --no-novel-juncs --GTF dmel-all-r6.03.gff --transcriptome-index dmel.transcriptome.tophat -o 9_GATCAG_L003_R1_001.tophat dmel.bowtie.index 9_GATCAG_L003_R1_001.fastq.gz | |
| samtools view -h 3_TTAGGC_L003_R1_001.tophat/accepted_hits.bam > 3_TTAGGC_L003_R1_001.tophat/accepted_hits.sam | |
| samtools view -h 4_TGACCA_L003_R1_001.tophat/accepted_hits.bam > 4_TGACCA_L003_R1_001.tophat/accepted_hits.sam | |
| samtools view -h 9_GATCAG_L003_R1_001.tophat/accepted_hits.bam > 9_GATCAG_L003_R1_001.tophat/accepted_hits.sam | |
| cufflinks -p 4 --GTF dmel-all-r6.03.gff -o 3_TTAGGC_L003_R1_001.cufflinks 3_TTAGGC_L003_R1_001.tophat/accepted_hits.sam | |
| cufflinks -p 4 --GTF dmel-all-r6.03.gff -o 4_TGACCA_L003_R1_001.cufflinks 4_TGACCA_L003_R1_001.tophat/accepted_hits.sam | |
| cufflinks -p 4 --GTF dmel-all-r6.03.gff -o 9_GATCAG_L003_R1_001.cufflinks 9_GATCAG_L003_R1_001.tophat/accepted_hits.sam | |
| echo 3_TTAGGC_L003_R1_001.cufflinks/transcripts.gtf >> assembly.gtfs | |
| echo 4_TGACCA_L003_R1_001.cufflinks/transcripts.gtf >> assembly.gtfs | |
| echo 9_GATCAG_L003_R1_001.cufflinks/transcripts.gtf >> assembly.gtfs | |
| cuffmerge -p 4 -g dmel-all-r6.02.gtf -s dmel-all-chromosome-r6.03.fasta -o assembly.cufflinks assembly.gtfs | |
| cuffquant -p 4 -o 3_TTAGGC_L003_R1_001.cuffquant assembly.cufflinks/merged.gtf 3_TTAGGC_L003_R1_001.tophat/accepted_hits.sam | |
| cuffquant -p 4 -o 4_TGACCA_L003_R1_001.cuffquant assembly.cufflinks/merged.gtf 4_TGACCA_L003_R1_001.tophat/accepted_hits.sam | |
| cuffquant -p 4 -o 9_GATCAG_L003_R1_001.cuffquant assembly.cufflinks/merged.gtf 9_GATCAG_L003_R1_001.tophat/accepted_hits.sam | |
| cuffdiff -p 4 -o geometric_norm.cuffdiff assembly.cufflinks/merged.gtf 3_TTAGGC_L003_R1_001.cuffquant/abundances.cxb 4_TGACCA_L003_R1_001.cuffquant/abundances.cxb 9_GATCAG_L003_R1_001.cuffquant/abundances.cxb |
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