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Hi everyone,
This is regarding RNA-seq Illumina mouse data of 75bp length between 2 samples states (with 2 replicates each) where a gene is knocked off and the other is the control. We are noticing very high variation in certain regions where coverage is very high. The regions exhibiting this behaviour have 10K + reads assigned to some exons. I also notice that the coverage is not uniform and certain exons are "bumped" up in all samples. I am wondering if others have noticed this before and what could be the reason for it? we have tried two different aligners (BWA and Bowtie), so it is probably not an alignment issue.
Thanks in advance.
This is regarding RNA-seq Illumina mouse data of 75bp length between 2 samples states (with 2 replicates each) where a gene is knocked off and the other is the control. We are noticing very high variation in certain regions where coverage is very high. The regions exhibiting this behaviour have 10K + reads assigned to some exons. I also notice that the coverage is not uniform and certain exons are "bumped" up in all samples. I am wondering if others have noticed this before and what could be the reason for it? we have tried two different aligners (BWA and Bowtie), so it is probably not an alignment issue.
Thanks in advance.