cufflinks

cufflinks

run cufflinks

the result of tophat is needed

~/Biosoft/cufflinks-2.2.1.Linux_x86_64/cufflinks -p 8 -b ../tophat/erecta.fna -u -o sample1 ../tophat/tophat_out/accepted_hits.bam

gtf merging

(without fasta.file result)

cuffmerge -o merged_asm -p 8 -s ../../tophat/erecta.fna list

cuffquant

(For count the reads)

cuffquant -o cuffquant2 -p 8 -b Genome.fna -u Genome.gff tophat.bam

##Exp:
cuffquant -o cuffquant2 -p 8 -b ../../data/Genome/A.japonicus/Apostichopus_japonicus.fna -u ../../data/Genome/A.japonicus/Apostichopus_japonicus.gff 2dpe/accepted_hits.bam                                      (the result of cuffquant is binary file you can run cuffnorm to transfor this binary file to readable file.)

cuffcompare

for stattistics (useless)

cuffcompare -o cuffcmp -r genome.gtf -s genome.fasta sample1.gtf

##Exp:
cuffcompare -o cuffcmp2 -r ../../data/Genome/A.japonicus/Apostichopus_japonicus.gff -s ../../data/Genome/A.japonicus/Apostichopus_japonicus.fna cufflinks2/transcripts.gtf

merge the fpkm

cuffnorm -L 0dpe,3dpe,7dpe,14dpe,21dpe -p 8 ../../data/Genome/A.japonicus/Apostichopus_japonicus.gff cuffquant2/abundances.cxb cuffquant3/abundances.cxb cuffquant4/abundances.cxb cuffquant5/abundances.cxb cuffquant6/abundances.cxb  -o cuffnorm

cuffdiff

… similar to the same as the cuffnorm.

cuffdiff -L A1,B2 -o cuffdiff2 -p 8 -u -b ../../data/Genome/A.japonicus/Apostichopus_japonicus.fna ../../data/Genome/A.japonicus/Apostichopus_japonicus.gff cuffquant2/abundances.cxb cuffquant2/abundances.cxb