Recently I aligned pair end MeDIP-seq reads using bowtie to hg19, I was confused about three problems although I had searched a lot of related posts.
1.I want to get the fragment of MeDIP-seq from the bam files, for the single end reads, after I aligned to ref genome, I extend my reads to the average fragment size for the following analysis. However, for paired end reads, the fragment could be accurate estimated by insert size. I want to know if existed some kinds of software for me to accomplish the job?
2.For my bam files, I want to get the uniquely mapped reads (fragment) for the following analysis, and this step is before or after the step of "get the fragment"? how do you achieve the goals? Please give me some advice.
3. Would you give me some pipeline or parameters when you process from the fastq files to unique mapped reads?
This is my first post and looking forward for your help! Many thanks.