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One repetition differs significantly
Dear SeqAnswer community,
I am working on an experiment in which we are doing RNAseq. We have 2 groups (a and p), each with three replicates. In one group, one repetition differs significantly from the others which is seen in the RNA-SeQC statistics (presented statistics after deduplication):
10000 Expressed Transcripts Sample Mean Per Base Cov. Mean CV
Bottom p1 3 0.92
Middle p1 4.36 0.83
Top p1 7.79 0.75
Bottom p2 3.63 0.87
Middle p2 5.28 0.79
Top p2 8.87 0.72
Bottom p3 3.43 0.9
Middle p3 4.98 0.82
Top p3 8.45 0.74
Bottom a1 5.46 1.08
Middle a1 5.71 1.07
Top a1 6.08 1.06
Bottom a2 7.2 0.82
Middle a2 9.47 0.77
Top a2 13.08 0.72
Bottom a3 8.13 0.8
Middle a3 10.03 0.77
Top a3 12.72 0.73
The other statistics like: Total Purity Filtered Reads Sequenced, Alternative Aligments, Estimated Library Size, Intragenic Rate, Exonic Rate, Intronic Rate, Intergenic Rate looks similar and overall alignment rate for bowtie looks similar for replicates.
My workflow: tophat -> cufflinks -> cuffmerge -> cuffdiff
The gene_exp.diff results for all replicates and without a1 differ in number of significant genes, from 405 to 168 differential expressed genes.
What I should do with a1 sample?
Thank you in advance for your help in this matter.
Kacper
I am working on an experiment in which we are doing RNAseq. We have 2 groups (a and p), each with three replicates. In one group, one repetition differs significantly from the others which is seen in the RNA-SeQC statistics (presented statistics after deduplication):
10000 Expressed Transcripts Sample Mean Per Base Cov. Mean CV
Bottom p1 3 0.92
Middle p1 4.36 0.83
Top p1 7.79 0.75
Bottom p2 3.63 0.87
Middle p2 5.28 0.79
Top p2 8.87 0.72
Bottom p3 3.43 0.9
Middle p3 4.98 0.82
Top p3 8.45 0.74
Bottom a1 5.46 1.08
Middle a1 5.71 1.07
Top a1 6.08 1.06
Bottom a2 7.2 0.82
Middle a2 9.47 0.77
Top a2 13.08 0.72
Bottom a3 8.13 0.8
Middle a3 10.03 0.77
Top a3 12.72 0.73
The other statistics like: Total Purity Filtered Reads Sequenced, Alternative Aligments, Estimated Library Size, Intragenic Rate, Exonic Rate, Intronic Rate, Intergenic Rate looks similar and overall alignment rate for bowtie looks similar for replicates.
My workflow: tophat -> cufflinks -> cuffmerge -> cuffdiff
The gene_exp.diff results for all replicates and without a1 differ in number of significant genes, from 405 to 168 differential expressed genes.
What I should do with a1 sample?
Thank you in advance for your help in this matter.
Kacper