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Hi everyone, this is my first post.
I have a question about analyzing satellite DNA transcripts. Would be great if someone has experience in this or some advice. It is known that satellite DNA expression increases after stress. We have two conditions, normal vs stress, and we know that this satellite DNA is in vicinity of several genes. For gene expression analysis I used DESeq2. Now we want to see transcript abundance of this satellite.
Would that be ok: align reads with bowtie2 to consensus satellite sequence, get mapped reads with samtools and calculate FPKM like: (mapped reads x 10e9) / (length of consensus sequence x total number of reads)?
I can see in our case that there are more reads in stress condition.
(paired-end 75 bp; consensus sequence around 350 bp)
Thanks for any feedback!
Antonio
I have a question about analyzing satellite DNA transcripts. Would be great if someone has experience in this or some advice. It is known that satellite DNA expression increases after stress. We have two conditions, normal vs stress, and we know that this satellite DNA is in vicinity of several genes. For gene expression analysis I used DESeq2. Now we want to see transcript abundance of this satellite.
Would that be ok: align reads with bowtie2 to consensus satellite sequence, get mapped reads with samtools and calculate FPKM like: (mapped reads x 10e9) / (length of consensus sequence x total number of reads)?
I can see in our case that there are more reads in stress condition.
(paired-end 75 bp; consensus sequence around 350 bp)
Thanks for any feedback!
Antonio