Skip to content

Instantly share code, notes, and snippets.

@rmihael

rmihael/gist:4ebc76e587db3ee4f2b8

Last active August 29, 2015 14:06
Show Gist options
  • Save rmihael/4ebc76e587db3ee4f2b8 to your computer and use it in GitHub Desktop.
Save rmihael/4ebc76e587db3ee4f2b8 to your computer and use it in GitHub Desktop.
Download ZIP
RNA-Seq differential expression
Raw
gistfile1.sh
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
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment