We did a ChIP-seq recently. Although the data looked OK, there is only ~2million tags mapped to the human genome, about 20% of the passed tags (per lane). Our bioinformatics guy did some analysis and found a lot tags matched with the adaptor sequences. For the library construction, we did size selection of 200-500bp fragments before 18cycles PCR amplication.
I am wondering what we can do to increase the mappable tags. Would it help if we repeat size selection and PCR amplification?
Thank you very much.
I am wondering what we can do to increase the mappable tags. Would it help if we repeat size selection and PCR amplification?
Thank you very much.
Comment