Dear all,
I am starting to work with Chip-seq data to identify binding sites of transcription factors and we have just received a test run from the company in order to decide to go ahead with the sequencing. We are using Hiseq. For a test run we got 100,000 reads of each library. We have sequenced for each sample the correspondent input. For the samples 40-50% reads mapped to the human genome (allowing max 2 mismaches) whereas the input had a percentage of mapped reads ~90% . I was expecting to obtain a lower percentage of mapped reads in the input and not in the sample. I used bowtie to make the alignment. I would like to know if someone as had similar percentages of mapped reads in Chip-seq experiments.
Thanks
Andreia
I am starting to work with Chip-seq data to identify binding sites of transcription factors and we have just received a test run from the company in order to decide to go ahead with the sequencing. We are using Hiseq. For a test run we got 100,000 reads of each library. We have sequenced for each sample the correspondent input. For the samples 40-50% reads mapped to the human genome (allowing max 2 mismaches) whereas the input had a percentage of mapped reads ~90% . I was expecting to obtain a lower percentage of mapped reads in the input and not in the sample. I used bowtie to make the alignment. I would like to know if someone as had similar percentages of mapped reads in Chip-seq experiments.
Thanks
Andreia
Comment