Difference between revisions of "Tuxedo pipeline"
From Crop Genomics Lab.
Sangrea Shim (Talk | contribs) (→Step 5. cuffmerge - merging gtf) |
Sangrea Shim (Talk | contribs) (→Step 2. bowtie build (align preprocessing)) |
||
| Line 4: | Line 4: | ||
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 ( | + | === Step 2. bowtie build (Build index file) === |
| − | bowtie-build | + | /location_of_bowtie/bowtie-build reference.fa reference.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) | ||
Revision as of 08:02, 11 April 2014
Contents |
Step 1. fastq dump
fastq-dump -A SRR203363 SRR203363.sra -A $sradata_accession $sra_data.sra if paired-end sequence file were used, we should use --split-3 option and check making *_1.fa and *_2.fa
Step 2. bowtie build (Build index file)
/location_of_bowtie/bowtie-build reference.fa reference.fa
Step 3. tophat - calculate splice junction
/data/program/tophat-1.4.1.Linux_x86_64/tophat -p 4(core) -G /data/ref/Gmax_189_gene.gff3 -o SRR203363_thout Gmax_189.fa(bowtie_index) SRR203363.fastq(reads)
Step 4. cufflinks - make gtf
cufflinks -p 4 -o ./SRR203363_clout(cufflinks_out_dir) SRR203363_thout/accepted_hits.bam(tophat_output)
Step 5. cuffmerge - merging gtf
- locations of transcripts.gtf files derived by cufflinks should be listed in assembly.txt
/location_of_cuffmerge/cuffmerge -g gff3_file_used_in_tophat -s reference.fa -p number_of_threads assemblies.txt
Step 6. cuffdiff - deg
/cuffdiff_location/cuffdiff \ -o out_dir \ -b reference.fa \ -p number_of_threads \ -L label_of_bam_1,label_of_bam_2 \ -u gtf_file_derived_by_cuffmerge \ bam_1 bam_2
Step 7. cummeRbund - analysis
- Execute R package in diff_out directory
/diff_out/$ R
- Import cummeRbund package
library(cummeRbund)
