Chip-Seq Analysis
Hi all,
I think I need some help:
We performed a Chip-Seq single read run of 36 cycles.
It was curious to verify that some of the libraries produced much more peaks.
We have 7 samples, and 3 off them generated libraries little concentrated. Of course we normalized library concentrations and we sequenced libraries with a final concentration of 12 pM. For all samples we obtained more than 150.000 clusters, 80% passed the quality filters and 72% aligned with the genomic reference. At the end we stay with more than 9 millions of reads per sample.
Finding peaks we obtained very different results: Samples that produced 10-30 ng/ul libraries produced much less peaks than samples which produced 2-4 ng/ul libraries.
I don’t know if there is some possible connection between initial library concentration and number of detected peaks. As we did a 12 pM dilution of all the samples and the number of reads is the same for all of them, it was difficult to find a connection, but… for other hand we can’t find a biological meaning for these differences.
Could you please give me an opinion?
Thank you very much!!!!
I think I need some help:
We performed a Chip-Seq single read run of 36 cycles.
It was curious to verify that some of the libraries produced much more peaks.
We have 7 samples, and 3 off them generated libraries little concentrated. Of course we normalized library concentrations and we sequenced libraries with a final concentration of 12 pM. For all samples we obtained more than 150.000 clusters, 80% passed the quality filters and 72% aligned with the genomic reference. At the end we stay with more than 9 millions of reads per sample.
Finding peaks we obtained very different results: Samples that produced 10-30 ng/ul libraries produced much less peaks than samples which produced 2-4 ng/ul libraries.
I don’t know if there is some possible connection between initial library concentration and number of detected peaks. As we did a 12 pM dilution of all the samples and the number of reads is the same for all of them, it was difficult to find a connection, but… for other hand we can’t find a biological meaning for these differences.
Could you please give me an opinion?
Thank you very much!!!!