We just ran a ChIP-seq sample on our GAII, just one lane. The sample was from a prokaryote and all indications are that the library prep and sequencing went well. We got ~16 million clusters, 8.6 million passed the default filtering. When we aligned the reads to the reference genome only ~50% of the filter passed reads aligned. We tried both Eland and MAQ, using default settings for both. We are just starting to work with ChIP so we don't have much in house experience to compare to. I guess my first questions are, what percentage of ChIP-seq reads are you typically able to align to your reference? Do you make any special adjustments to alignment parameters when working with ChIP data?
Thanks in advance.
Thanks in advance.
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