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!
Try BWA with just one file, over even a subset of your reads. BWA will estimate insert size from the mapping, and its output may help you understand what went wrong with your Bowtie mapping. If you want to stick with Bowtie / Bowtie2, you then may use BWA estimated mean and sd insert size values as input for Bowtie.
I can estimate the average DNA fragment length as ~150 based on the reads which successfully aligned