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Old 08-30-2013, 02:22 AM   #1
Alex234
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Location: UK

Join Date: Aug 2013
Posts: 31
Default Decreased transcription of short intergenic patches - a common artefact?

Hello, I've compared transcription between a WT and KO ES cell line by RNA-Seq using DESeq and a GTF file assembled from cufflinks and have found a decrease in the transcription of many short intergenic regions (they only have XLOC ids, and having checked in genome browsers there do not seem to be any genes there). So my questions are:

(a) Is this some sort of common artefact?

(b) How can I look at how the reads are actually assembled within each of those regions, and would that tell me whether they are actually being transcribed or if it's just some sort of artefact?

(c) When ranked by fold change (and with a cut off of p<0.05) these short sequences are ranked near the top of the downregulated genes, but when ranked by p-value, they rank less highly - general thoughts on ranking DEGs by fold change vs. p-value?


Thanks

Alex
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