Difference between revisions of "Tuxedo pipeline"
(Created page with "===Step 1. fastq dump === fastq-dump -A SRR203363 SRR203363.sra -A $sradata_accession $sra_data.sra if paired-end sequence file were used, we should use --split-3 optio...") |
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| − | ===Step 1. fastq dump === | + | === Step 1. fastq dump === |
fastq-dump -A SRR203363 SRR203363.sra | fastq-dump -A SRR203363 SRR203363.sra | ||
-A $sradata_accession $sra_data.sra | -A $sradata_accession $sra_data.sra | ||
if paired-end sequence file were used, we should use --split-3 option and check making *_1.fa and *_2.fa | if paired-end sequence file were used, we should use --split-3 option and check making *_1.fa and *_2.fa | ||
| − | ===Step 2. bowtie build (align preprocessing) === | + | === Step 2. bowtie build (align preprocessing) === |
bowtie-build Gmax_189.fa Gmax_189.fa | bowtie-build Gmax_189.fa Gmax_189.fa | ||
| − | ===Step 3. tophat - calculate splice junction === | + | === Step 3. tophat - calculate splice junction === |
/data/program/tophat-1.4.1.Linux_x86_64/tophat -p 4(core) -G /data/ref/Gmax_189_gene.gff3 -o SRR203363_thout Gmax_189.fa(bowtie_index) SRR203363.fastq(reads) | /data/program/tophat-1.4.1.Linux_x86_64/tophat -p 4(core) -G /data/ref/Gmax_189_gene.gff3 -o SRR203363_thout Gmax_189.fa(bowtie_index) SRR203363.fastq(reads) | ||
| − | ===Step 4. cufflinks - make gtf === | + | === Step 4. cufflinks - make gtf === |
cufflinks -p 4 -o ./SRR203363_clout(cufflinks_out_dir) SRR203363_thout/accepted_hits.bam(tophat_output) | cufflinks -p 4 -o ./SRR203363_clout(cufflinks_out_dir) SRR203363_thout/accepted_hits.bam(tophat_output) | ||
| − | ===Step 5. cuffmerge - merging gtf === | + | === Step 5. cuffmerge - merging gtf === |
in the assemblies.txt, file location such as ./SRR####_clout/transcripts.gtf should be written in each line | in the assemblies.txt, file location such as ./SRR####_clout/transcripts.gtf should be written in each line | ||
/data/program/cufflinks-2.1.1.Linux_x86_64/cuffmerge -g /data/ref/Gmax_189_gene.gff3(used_at_tophat) -s ./Gmax_189.fa(bowtie_indexed_genome_fasta) -p 4 ./assemblies.txt | /data/program/cufflinks-2.1.1.Linux_x86_64/cuffmerge -g /data/ref/Gmax_189_gene.gff3(used_at_tophat) -s ./Gmax_189.fa(bowtie_indexed_genome_fasta) -p 4 ./assemblies.txt | ||
| − | ===Step 6. cuffdiff - deg === | + | === Step 6. cuffdiff - deg === |
/data/program/cufflinks-2.1.1.Linux_x86_64/cuffdiff -o ./diff_out/ -b Gmax_189.fa -p 4 -L w82Leaf,w82leaf -u ./merged_asm/merged.gtf ./SRR203363_thout/accepted_hits.bam ./SRR203363_thout/accepted_hits.bam | /data/program/cufflinks-2.1.1.Linux_x86_64/cuffdiff -o ./diff_out/ -b Gmax_189.fa -p 4 -L w82Leaf,w82leaf -u ./merged_asm/merged.gtf ./SRR203363_thout/accepted_hits.bam ./SRR203363_thout/accepted_hits.bam | ||
| − | ===Step 7. cummeRbund - analysis === | + | === Step 7. cummeRbund - analysis === |
R | R | ||
Library(cummeRbund) | Library(cummeRbund) | ||
Diff-> | Diff-> | ||
Revision as of 07:47, 10 March 2014
Contents |
Step 1. fastq dump
fastq-dump -A SRR203363 SRR203363.sra -A $sradata_accession $sra_data.sra if paired-end sequence file were used, we should use --split-3 option and check making *_1.fa and *_2.fa
Step 2. bowtie build (align preprocessing)
bowtie-build Gmax_189.fa Gmax_189.fa
Step 3. tophat - calculate splice junction
/data/program/tophat-1.4.1.Linux_x86_64/tophat -p 4(core) -G /data/ref/Gmax_189_gene.gff3 -o SRR203363_thout Gmax_189.fa(bowtie_index) SRR203363.fastq(reads)
Step 4. cufflinks - make gtf
cufflinks -p 4 -o ./SRR203363_clout(cufflinks_out_dir) SRR203363_thout/accepted_hits.bam(tophat_output)
Step 5. cuffmerge - merging gtf
in the assemblies.txt, file location such as ./SRR####_clout/transcripts.gtf should be written in each line
/data/program/cufflinks-2.1.1.Linux_x86_64/cuffmerge -g /data/ref/Gmax_189_gene.gff3(used_at_tophat) -s ./Gmax_189.fa(bowtie_indexed_genome_fasta) -p 4 ./assemblies.txt
Step 6. cuffdiff - deg
/data/program/cufflinks-2.1.1.Linux_x86_64/cuffdiff -o ./diff_out/ -b Gmax_189.fa -p 4 -L w82Leaf,w82leaf -u ./merged_asm/merged.gtf ./SRR203363_thout/accepted_hits.bam ./SRR203363_thout/accepted_hits.bam
Step 7. cummeRbund - analysis
R Library(cummeRbund) Diff->
