Created
April 5, 2016 13:23
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##Shell script for running tophat2 and cuffdiff | |
##Place in /home/bioinfo/Data/test_RNAseq to use | |
#Step 1: run index the reference fasta file for faster match searching | |
bowtie2-build bwt2_index/SL2.40ch04.fa bwt2_index/SL2.40ch04 | |
#Step 2: run tophat2 on first breaker fastq file | |
tophat2 -o fastq/breaker/SRR404334_ch4_thout --no-novel-juncs --no-coverage-search bwt2_index/SL2.40ch04 fastq/breaker/SRR404334_ch4.fastq | |
#Step 3: run tophat2 on second breaker fastq file | |
tophat2 -o fastq/breaker/SRR404336_ch4_thout --no-novel-juncs --no-coverage-search bwt2_index/SL2.40ch04 fastq/breaker/SRR404336_ch4.fastq | |
#Step 4: run tophat2 on first immature fruit fastq file | |
tophat2 -o fastq/immature_fruit/SRR404331_ch4_thout --no-novel-juncs --no-coverage-search bwt2_index/SL2.40ch04 fastq/immature_fruit/SRR404331_ch4.fastq | |
#Step 5: run tophat2 on second immature fruit fastq file | |
tophat2 -o fastq/immature_fruit/SRR404333_ch4_thout --no-novel-juncs --no-coverage-search bwt2_index/SL2.40ch04 fastq/immature_fruit/SRR404333_ch4.fastq | |
#Step 6: run cufflinks to find putatively differential expressed genes | |
cuffdiff -o cuffdiff_out -b bwt2_index/SL2.40ch04.fa -u annotation/ITAG2.3_gene_models_ch4.gtf fastq/breaker/SRR404334_ch4_thout/accepted_hits.bam,fastq/breaker/SRR404336_ch4_thout/accepted_hits.bam fastq/immature_fruit/SRR404331_ch4_thout/accepted_hits.bam,fastq/immature_fruit/SRR404333_ch4_thout/accepted_hits.bam |
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