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===Further examination of the data quality=== *I first create a master transcripts.gtf file that combined all transcripts found in the 13 data sets. /home/kunzhang/softwares/cufflinks-1.0.3.Linux_x86_64/cuffcompare -o cuffcompare_all -R tophat_Mm_Indx3/transcripts.gtf tophat_Mm_Indx4/transcripts.gtf ... tophat_Mm_Indx15/transcripts.gtf *Then I ran cuffdiff on technical/biological replicates to examine the noise in the data. /home/kunzhang/softwares/cufflinks-1.0.3.Linux_x86_64/cuffdiff cuffcompare_all.combined.gtf -N -p 8 -o cuffDiff_3_vs_7 tophat_Mm_Indx3/accepted_hits.bam tophat_Mm_Indx7/accepted_hits.bam /home/kunzhang/softwares/cufflinks-1.0.3.Linux_x86_64/cuffdiff cuffcompare_all.combined.gtf -N -p 8 -o cuffDiff_4_vs_8 tophat_Mm_Indx4/accepted_hits.bam tophat_Mm_Indx8/accepted_hits.bam /home/kunzhang/softwares/cufflinks-1.0.3.Linux_x86_64/cuffdiff cuffcompare_all.combined.gtf -N -p 8 -o cuffDiff_9_vs_10 tophat_Mm_Indx9/accepted_hits.bam tophat_Mm_Indx10/accepted_hits.bam /home/kunzhang/softwares/cufflinks-1.0.3.Linux_x86_64/cuffdiff cuffcompare_all.combined.gtf -N -p 8 -o cuffDiff_14_vs_15 tophat_Mm_Indx14/accepted_hits.bam tophat_Mm_Indx15/accepted_hits.bam /home/kunzhang/softwares/cufflinks-1.0.3.Linux_x86_64/cuffdiff cuffcompare_all.combined.gtf -N -p 8 -o cuffDiff_5_vs_9 tophat_Mm_Indx5/accepted_hits.bam tophat_Mm_Indx9/accepted_hits.bam /home/kunzhang/softwares/cufflinks-1.0.3.Linux_x86_64/cuffdiff cuffcompare_all.combined.gtf -N -p 8 -o cuffDiff_6_vs_11 tophat_Mm_Indx6/accepted_hits.bam tophat_Mm_Indx11/accepted_hits.bam /home/kunzhang/softwares/cufflinks-1.0.3.Linux_x86_64/cuffdiff cuffcompare_all.combined.gtf -N -p 8 -o cuffDiff_11_vs_12 tophat_Mm_Indx11/accepted_hits.bam tophat_Mm_Indx12/accepted_hits.bam *Then I plotted the FPKM values between each pairs of replicates. Between two batches of experiments: R=0.939 R=0.928 [[Image:FPKM_Indx3_vs_Indx7.png|300px]][[Image:FPKM_Indx4_vs_Indx8.png|300px]] R=0.935 R=0.978 [[Image:FPKM_Indx5_vs_Indx9.png|300px]][[Image:FPKM_Indx6_vs_Indx11.png|300px]] Within one batch of experiment. R=0.911 R=0.984 [[Image:FPKM_Indx9_vs_Indx10.png|300px]][[Image:FPKM_Indx11_vs_Indx12.png|300px]] R=0.552 (a few transcripts seem to be missing in one sample) [[Image:FPKM_Indx14_vs_Indx15.png|300px]]
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