Difference between revisions of "Tuxedo pipeline"
From Crop Genomics Lab.
Sangrea Shim (Talk | contribs) (→Step 6. cuffdiff - deg) |
Sangrea Shim (Talk | contribs) (→Step 6. cuffdiff - deg) |
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-p number_of_threads \ | -p number_of_threads \ | ||
-L label_of_bam_1,label_of_bam_2 \ | -L label_of_bam_1,label_of_bam_2 \ | ||
− | -u gtf_file_derived_by_cuffmerge \ | + | -u gtf_file_derived_by_cuffmerge(merged_asm/transcript.gtf) \ |
tophat_out_dir/accepted_hits.bam_1 tophat_out_dir/accepted_hits.bam_2 | tophat_out_dir/accepted_hits.bam_1 tophat_out_dir/accepted_hits.bam_2 | ||
Revision as of 08:12, 11 April 2014
Contents |
Step 1. fastq dump
fastq-dump -A SRR203363 SRR203363.sra -A $sradata_accession $sra_data.sra if paired-end sequence file were used, we should use --split-3 option and check making *_1.fa and *_2.fa
Step 2. bowtie build (Build index file)
/location_of_bowtie/bowtie-build reference.fa reference.fa
Step 3. tophat (calculate splice junction)
/loaction_of_tophat/tophat -p number_of_threads \ -G gff3_file_of_genome \ -o tophat_ouput_dir \ reference.fa \ fastq_file
Step 4. cufflinks - make gtf
/location_of_cufflinks/cufflinks -p number_of_threads \ -o cufflinks_out_dir \ tophat_out_dir/accepted_hits.bam
Step 5. cuffmerge - merging gtf
- locations of transcripts.gtf files derived by cufflinks should be listed in assembly.txt
* in assembly.txt cufflinks_out_dir/transcript.gtf cufflinks_out_dir/transcript.gtf
/location_of_cuffmerge/cuffmerge -g gff3_file_used_in_tophat \ -s reference.fa \ -p number_of_threads assemblies.txt
Step 6. cuffdiff - deg
/cuffdiff_location/cuffdiff \ -o cuffdiff_out_dir \ -b reference.fa \ -p number_of_threads \ -L label_of_bam_1,label_of_bam_2 \ -u gtf_file_derived_by_cuffmerge(merged_asm/transcript.gtf) \ tophat_out_dir/accepted_hits.bam_1 tophat_out_dir/accepted_hits.bam_2
Step 7. cummeRbund - analysis
- Execute R package in diff_out directory
/diff_out/$ R
- Import cummeRbund package
library(cummeRbund)