Hello everyone
We are using BAM to map Illumina reads to a bacterial genome, followed by Cufflinks to get the FPKMs (implemented in Galaxy). We have come across many genes for which we get FPKM=0 (using both gene and transcript expression) even though there are reads mapping to these gene IDs (when we visualize using IGV).
The genes which have"0 FPKM" have different tags: some are LOWDATA, some are HIDATA and some are OK...
We tried changing the number of reads used as input into Cufflinks - when we used many reads (~12,000,000 on a genome with ~2,400 genes) most of the genes have 0 FPKM and "HIDATA". When we used fewer reads (1,000,000) on the same genome many of the genes still had "0 FPKM" but now with different flags (OK or LOWDATA).
We tried using quartile normalization and this didn't seem to help much.
Why is Cufflinks saying there is no expression from expressed genes? Can anyone suggest a reason/fix for this?
Thanks
Daniel
We are using BAM to map Illumina reads to a bacterial genome, followed by Cufflinks to get the FPKMs (implemented in Galaxy). We have come across many genes for which we get FPKM=0 (using both gene and transcript expression) even though there are reads mapping to these gene IDs (when we visualize using IGV).
The genes which have"0 FPKM" have different tags: some are LOWDATA, some are HIDATA and some are OK...
We tried changing the number of reads used as input into Cufflinks - when we used many reads (~12,000,000 on a genome with ~2,400 genes) most of the genes have 0 FPKM and "HIDATA". When we used fewer reads (1,000,000) on the same genome many of the genes still had "0 FPKM" but now with different flags (OK or LOWDATA).
We tried using quartile normalization and this didn't seem to help much.
Why is Cufflinks saying there is no expression from expressed genes? Can anyone suggest a reason/fix for this?
Thanks
Daniel
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