whole exome sequence fragment size analysis

Question

[adR]

Hi everyone, I have aligned bam files with the reference genome. All reads are single reads. I want to analyze fragment size using bamPEFragmentSize. My questions are as follows: How does it work for single reads?. Because while running the program I saw a message says No pairs were found. Is the data from a paired-end sequencing experiment?

1. I find that bamPEFragmentSize read the sorted bam in my case. Do I need to pass the unsorted bam file instead of the sorted bam file? regards adr

Answer 1

[ATpoint]

How does it work for single reads

It does not. Single-end is not paired-end, simple as that.

[adR]

ATpoint , I greatly appreciate your response. But do you any tool that does this kind of analysis?

[ATpoint]

It is not a tool question. Think of it that way, you are trying to hammer a nail into the wall. You have 10 different hammers, but no nail. You cannot nail something without nails. Same here, you want insert size stats and have no insert sizes because it is single-end. At best you can ask the people who made the library for the details on the fragment size assessed by bioanalyzer or gel electrophoresis. You do not have the data to analyse what you want to analyze.

[adR]

ATpoint Thank you for the advice!