It works using ucsc genome gft file
1) cufflinks
/home/xusheng/Biosoft/cufflinks-1.0.3.Linux_x86_64/cufflinks -p 16 -g /home/xusheng/GenomeSequence/Human/refGene.gtf -o AD1 AD1_accepted_hits.bam
2) cuffcompare
/home/xusheng/Biosoft/cufflinks-1.0.3.Linux_x86_64/cuffcompare -V -r /home/xusheng/GenomeSequence/Human/refGene.gtf -s /home/xusheng/GenomeSequence/Human/hg19.fa -R -o s7_s8_refGene AD1/transcripts.gtf Nor3/transcripts.gtf
3. cuffdiff
home/xusheng/Biosoft/cufflinks-1.0.3.Linux_x86_64/cuffdiff -p 16 s7_s8_refGene.combined.gtf AD1/AD1_accepted_hits.bam Nor3/Nor3_accepted_hits.bam
4 comments:
/home/xusheng/Biosoft/cufflinks-1.0.3.Linux_x86_64/cuffcompare -V -r /home/xusheng/GenomeSequence/Human/refGene.gtf -s /home/xusheng/GenomeSequence/Human/hg19.fa -R -o AD13467_Nor3457_refGene AD1/transcripts.gtf AD3/transcripts.gtf AD4/transcripts.gtf AD6/transcripts.gtf AD7/transcripts.gtf Nor3/transcripts.gtf Nor4/transcripts.gtf Nor5/transcripts.gtf Nor7/transcripts.gtf
home/xusheng/Biosoft/cufflinks-1.0.3.Linux_x86_64/cuffdiff -p 16 ad13467_nor3467_refGene.combined.gtf AD1/AD1_accepted_hits.bam,AD3/AD3_accepted_hits.bam,AD4/AD4_accepted_hits.bam,AD6/AD6_accepted_hits.bam,AD7/AD7_accepted_hits.bam Nor3/Nor3_accepted_hits.bam,Nor4/Nor4_accepted_hits.bam,Nor6/Nor6_accepted_hits.bam,Nor7/Nor7_accepted_hits.bam
export PATH=/home/xusheng/Biosoft/cufflinks-1.0.3.Linux_x86_64/:$PATH
grep 'yes' cds.diff >cds.diff_yes
grep 'yes' cds_exp.diff >cds_exp.diff_yes
grep 'yes' gene_exp.diff >gene_exp.diff_yes
grep 'yes' isoform_exp.diff >isoform_exp.diff_yes
grep 'yes' promoters.diff >promoters.diff_yes
grep 'yes' splicing.diff >splicing.diff_yes
grep 'yes' tss_group_exp.diff >tss_group_exp.diff_yes
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