Hi I ran htseq on a number of RNA expression data, but I get a read count of zero for a certain transcript which I am sure should not be zero. The data are generated from multiple samples in multiple batches in multiple labs, so it's very unlikely that the data is wrong.
I would highly appreciate your expert opinion. What could possibly the reason for the count to be zero whereas I know this is the gene of interest and it should be expressed at various degrees in the different datasets of mine.
I generated a wiggle file from the bam and checked the number of peaks for the region of interest, there are peaks in the region (even though very weak at >50% positions).
Thanks!
I would highly appreciate your expert opinion. What could possibly the reason for the count to be zero whereas I know this is the gene of interest and it should be expressed at various degrees in the different datasets of mine.
I generated a wiggle file from the bam and checked the number of peaks for the region of interest, there are peaks in the region (even though very weak at >50% positions).
Thanks!
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