Question: Find Fragment Size of a bamfilee
1
gravatar for GK1610
13 months ago by
GK161020
United States
GK161020 wrote:

I have a test.bam file which has paired end reads data

I want to find the fragment size of each pair to compare the results from macs2 fragment size determination.

chip-seq • 443 views
ADD COMMENTlink modified 13 months ago by apnri40 • written 13 months ago by GK161020

Starting with your original data you can calculate the insert sizes by a couple of different ways using BBMap. BBMap is available here.

ADD REPLYlink written 13 months ago by genomax37k
1
gravatar for Devon Ryan
13 months ago by
Devon Ryan73k
Freiburg, Germany
Devon Ryan73k wrote:

You can get the distribution with bamPEFragmentSize from deepTools.

ADD COMMENTlink written 13 months ago by Devon Ryan73k
1
gravatar for apnri
13 months ago by
apnri40
apnri40 wrote:

Fragment size calculation is usually determined by cross-correlation analysis, wherein you compute correlation between the positive and negative strand densities from a particular position. Then you shift the position of both strands by one position - you should expect to see maximum correlation between the two strands at fragment length.

You can use spp (used by ENCODE consortium) package to do this in R.

Snippet of code:

library(spp)    
chip.data <- read.bam.tags(bamfile)
binding.characteristics <- get.binding.characteristics(chip.data,srange=c(50,500),bin=5, accept.all.tags = T)
print(paste("binding peak separation distance =",binding.characteristics$peak$x))
ADD COMMENTlink modified 13 months ago • written 13 months ago by apnri40

This is only done for single-end data (otherwise, the fragment length distribution can simply be measured) and the ENCODE cross-correlation stuff is...incredibly questionable (the amount of filter and mucking with the data that's done to get the results is, frankly, absurd).

ADD REPLYlink written 13 months ago by Devon Ryan73k
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