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cufflinks

run cufflinks

the result of tophat is needed

  1. ~/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)

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

cuffquant

(For count the reads)

  1. cuffquant -o cuffquant2 -p 8 -b Genome.fna -u Genome.gff tophat.bam
  3. ##Exp:
  4. 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)

  1. cuffcompare -o cuffcmp -r genome.gtf -s genome.fasta sample1.gtf
  3. ##Exp:
  4. 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

  1. 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.

  1. 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

Enjoy~

本文由Python腳本GitHub/語雀自動更新

由於語法渲染問題而影響閱讀體驗， 請移步博客閱讀～
本文GitPage地址

GitHub: Karobben
Blog:Karobben
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