I have used bowtie to map my reads against Arabidopsis.
I have also built a reference genome out of my luciferase gene sequence and did map my reads against that.
I'm wondering whether building bowtie indexes out of that short sequence will affect my further analysis?
Do you think that after applying the same way of normalization (in my case for total read number and for gene length) I will have comparable results between luciferase and Arabidopsis?
In luciferase case my number of mapped reads will be equal to total reads mapped so doing this normalization does not make a lot of sense.
RPKM maybe?
I have also built a reference genome out of my luciferase gene sequence and did map my reads against that.
I'm wondering whether building bowtie indexes out of that short sequence will affect my further analysis?
Do you think that after applying the same way of normalization (in my case for total read number and for gene length) I will have comparable results between luciferase and Arabidopsis?
In luciferase case my number of mapped reads will be equal to total reads mapped so doing this normalization does not make a lot of sense.
RPKM maybe?
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