Anton Kulaga antonkulaga
rmihael
/ gist:4ebc76e587db3ee4f2b8
Last active
August 29, 2015 14:06
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_L00 |