How to extract unique mapped reads from your bam files?

Question

[343924049]

Hi, guys!

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.

[Pavel Senin]

I think these [simple] questions were asked before and you can find answers easily. Here is the one about uniquely mapped reads and about the insert size estimation.

[343924049]

Thank you for your rely!

I have carefully read the post, the following fomat is what I want from my bam file(pair end reads)

name start end
chr1 100 300
chr1 120 330
...

that is each row represent a fragment. I know how to convert bam to bed format, the main confusion is how to get each fragment? Need I to refer the TLEN of sam files?