Hello, Could you please advise on the following:
We have ChIP-seq data with paired-end Illumina reads. For some of the samples only about 11% or reads could be mapped with Bowtie. When remapping these samples with Bowtie2, up to 85% reads could be mapped, but the pairs have been lost, meaning that for most mapped reads there is no pair available. What could go wrong and how to fix it? Thanks!