Difference between revisions of "Tuxedo pipeline"
From Crop Genomics Lab.
Sangrea Shim (Talk | contribs) (→Step 2. bowtie build (align preprocessing)) |
Sangrea Shim (Talk | contribs) (→Step 3. tophat - calculate splice junction) |
||
Line 7: | Line 7: | ||
/location_of_bowtie/bowtie-build reference.fa reference.fa | /location_of_bowtie/bowtie-build reference.fa reference.fa | ||
− | === Step 3. tophat | + | === Step 3. tophat (calculate splice junction) === |
− | / | + | /loaction_of_tophat/tophat -p number_of_threads \ |
− | + | -G gff3_file_of_genome \ | |
+ | -o ouput_dir \ | ||
+ | reference.fa \ | ||
+ | fastq_file | ||
+ | |||
=== 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) |
Revision as of 08:05, 11 April 2014
Contents |
Step 1. fastq dump
fastq-dump -A SRR203363 SRR203363.sra -A $sradata_accession $sra_data.sra if paired-end sequence file were used, we should use --split-3 option and check making *_1.fa and *_2.fa
Step 2. bowtie build (Build index file)
/location_of_bowtie/bowtie-build reference.fa reference.fa
Step 3. tophat (calculate splice junction)
/loaction_of_tophat/tophat -p number_of_threads \ -G gff3_file_of_genome \ -o ouput_dir \ reference.fa \ fastq_file
Step 4. cufflinks - make gtf
cufflinks -p 4 -o ./SRR203363_clout(cufflinks_out_dir) SRR203363_thout/accepted_hits.bam(tophat_output)
Step 5. cuffmerge - merging gtf
- locations of transcripts.gtf files derived by cufflinks should be listed in assembly.txt
/location_of_cuffmerge/cuffmerge -g gff3_file_used_in_tophat -s reference.fa -p number_of_threads assemblies.txt
Step 6. cuffdiff - deg
/cuffdiff_location/cuffdiff \ -o out_dir \ -b reference.fa \ -p number_of_threads \ -L label_of_bam_1,label_of_bam_2 \ -u gtf_file_derived_by_cuffmerge \ bam_1 bam_2
Step 7. cummeRbund - analysis
- Execute R package in diff_out directory
/diff_out/$ R
- Import cummeRbund package
library(cummeRbund)