Hi to all
I have RNA -seq data, for calculation of FPKM value manually, we should need to know no of fragments were generated during RNA-seq for given gene am I right? Please any one tell me where to look to get the no of fragments produced for a given gene or any feature liks cds etc.,
I followed one procedure Please let me know if my way of knowing read is wrong?
first i open bam files into IGV , then I calculate the no of fragments for a given gene. Whether I did a right? and also please tell if above procedure is right for pair end sequencing whether i have to count both left and right fragments separately or combine into 1.
I have RNA -seq data, for calculation of FPKM value manually, we should need to know no of fragments were generated during RNA-seq for given gene am I right? Please any one tell me where to look to get the no of fragments produced for a given gene or any feature liks cds etc.,
I followed one procedure Please let me know if my way of knowing read is wrong?
first i open bam files into IGV , then I calculate the no of fragments for a given gene. Whether I did a right? and also please tell if above procedure is right for pair end sequencing whether i have to count both left and right fragments separately or combine into 1.
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