I have received data where one (or more) of the steps ChIP-Seq has failed :
There was a large difference between the amount of reads generated for IP and for Input samples (3-5 million reads for IP, 20-30 million reads for Input).
The sequencing was paired-end. For the IP samples, R1 had a large amount of adapters (around 30% of the data did not pass the filtering stage, mainly due to adapter content). R2 did not have such a large percentage of adapters, but around 30% of the reads did not pass the filtering stage due to bad quality.
Input samples did not have this problem.
When aligning, Read 2 of the IP samples did not have a higher percentage of unique alignment than 20%.
( R1 of the IP was uniquely aligned around 50% - 70%, with the input samples being aligned at a 75% rate.)
At the end, even for R1, there are only about 500K - 1 million reads uniquely aligned per each IP sample.
So, basically there is no data to work with.
What I would like to do however, is to understand whether the failure was (1) during the ChIP stage (2) During transit of the samples (the DNA was in transit around 10 days). (3) Library preparation.
Can you suggest how it can be checked, in case it can be?
Preparing the libraries anew / resequencing is currently not possible, unfortunately.