Hi everyone,
I have RNA seq data from the same tissue under 2 different experimental conditions and Im trying to find differentially regulated transcripts. I've used Cufflinks/ Cuffdiff to calculate FPKM values and find differentially expressed transcripts. From what I understand, Cufflinks does not run the statistical test in cases where there is low coverage, and many of the transcripts in my samples have low read counts. Also, a couple of my control transcripts have very small fold changes which are not being detected to be significant by Cufflinks. I might be missing detecting small but significant fold changes.
I would really appreciate any ideas on other programs/ statistical tests that I can use to calculate significance in small fold changes.
I have RNA seq data from the same tissue under 2 different experimental conditions and Im trying to find differentially regulated transcripts. I've used Cufflinks/ Cuffdiff to calculate FPKM values and find differentially expressed transcripts. From what I understand, Cufflinks does not run the statistical test in cases where there is low coverage, and many of the transcripts in my samples have low read counts. Also, a couple of my control transcripts have very small fold changes which are not being detected to be significant by Cufflinks. I might be missing detecting small but significant fold changes.
I would really appreciate any ideas on other programs/ statistical tests that I can use to calculate significance in small fold changes.
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