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Dear All,
I am running Cufflinks on RNAseq data from 2 samples. The parameters I have used for both the samples are
--frag-bias-correct --library-type fr-unstranded --upper-quartile-norm --no-effective-length-correction
A particular locus has differential expression for Sample2 (higher expression) as compared to Sample1. On individually loading the assembled trasncripts from each sample I observed that the transcript model built by Cuffmerge is finally coming from Sample1 while there is nothing in Sample2. This is an isolated incident amongst 200 differential trasncripts.
Cufflinks built the trasncript model from the less abundant sample for that locus, while completely ignoring the locus in the more abundant sample.
My question is that whether this can be a random calculation mistake on part of Cufflinks, or I need to to give a look into a particular parameter. I have attached a screenshot of the RNAseq peaks and trasncripts build by cufflinks for both the samples.
Thanks in advance.
I am running Cufflinks on RNAseq data from 2 samples. The parameters I have used for both the samples are
--frag-bias-correct --library-type fr-unstranded --upper-quartile-norm --no-effective-length-correction
A particular locus has differential expression for Sample2 (higher expression) as compared to Sample1. On individually loading the assembled trasncripts from each sample I observed that the transcript model built by Cuffmerge is finally coming from Sample1 while there is nothing in Sample2. This is an isolated incident amongst 200 differential trasncripts.
Cufflinks built the trasncript model from the less abundant sample for that locus, while completely ignoring the locus in the more abundant sample.
My question is that whether this can be a random calculation mistake on part of Cufflinks, or I need to to give a look into a particular parameter. I have attached a screenshot of the RNAseq peaks and trasncripts build by cufflinks for both the samples.
Thanks in advance.