Hello I have the human chip seq data on which I want to perform the chip seqanalysis. I have done the alignment of the data with the human genome and also with the drosophila melangoaster genome and also removed the duplicates. I want to apply the spike in method to normalize the reads but I couldnt figure out how to implement it . in the paper that I am trying to implement its mentioned to count the tags in each sample/spike genome and using the tag counts find a correction factor calculated as DMSO tags/inhibitor tags.
DOes that mean I should call in the peaks for samples aligned to human genome and for the samples aligned to the fruit fly genome separately and count the tags and apply the correction factor ??
Any guidance / suggestions are welcomed . I have a computer science background so if its a naive question please bare with me .
Thankyou so much
Mehvi
