Dear users
I tried to calculate the mean sequencing depth of RNA-seq. Firstly, I utilized GATK to calculate that with the whole genome as reference. It turned out that some samples with around 15 million mapped reads only have around 2.5* mean sequencing depth. That looks to me weird. Some people suggested me to calculate it by hand, such as: (number of mapped reads * read length)/total length of the species' transcriptome
It looks reasonable. How do you calculate the sequencing depth of RNA-seq?
I will appreciate your comments very much!
I tried to calculate the mean sequencing depth of RNA-seq. Firstly, I utilized GATK to calculate that with the whole genome as reference. It turned out that some samples with around 15 million mapped reads only have around 2.5* mean sequencing depth. That looks to me weird. Some people suggested me to calculate it by hand, such as: (number of mapped reads * read length)/total length of the species' transcriptome
It looks reasonable. How do you calculate the sequencing depth of RNA-seq?
I will appreciate your comments very much!
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