how to quantification of paired end reads

Question

[Raghav]

I have download the hiC data from NCBI and nd instead of mapping them on reference genome, I mapped the data on list of genes separately. it means I mapped the R1 and R2 separately.

Now I want quantify how many reads are their hows R1 part are mapped on gene1 (suppose) and R2 part on gene 2.

for example

if total number of reads are 100 (50 R1 and 50 R2). total number of genes are 5 (suppose). out of 100 reads, 30 reads (R1/R2) are mapped on gene1. then find out counter part of reads (R2/R1) which mapped apart from gene1..

positive suggestions are always welcome

Answer 1

[Prakki Rama]

Try running BLAT. You should be able to compare the table output.

Answer 2

[mikhail.shugay]

I suggest that with current state of Hi-C technology, it is better to use the normalized data, not the raw one. For the resolution considerations, it is also better to bin Hi-C data by 1Mb/500kb bins and for a pair of genes compare the Hi-C value for pairs of bins in which those genes are positioned.

You can download normalized Hi-C contact maps here:

http://compgenomics.weizmann.ac.il/tanay/?page_id=283