Using Chromosome conformation capture Data for DEG in circadian gene

Question

[sabaghianamir70]

Hey Guys

I want to get count from a circadian gene which is PER4. it is PER3s pseudogene. So i used Salmon and ive got Per3 not per4 Counts. But i saw some data in same paper which the name was Chromosome conformation capture(Hi-C) which has Counts in per4. So is this right to do DEG on Hi-C instead of RNA seq data

P.s both RNA seq and Hi-C data make from illumina1.9

Answer 1

[ATpoint]

This does not make any sense as both assays investigate fundamentally different things. Hi-C measures interaction frequencies between genomic loci while RNA-seq quantifies transcripts in a given population of cells. Mixing them is completely pointless. Illumina 1.9 by the way is simply the format in which the quality scores are encoded in the fastq file, it does not tell you anything about comparability.

[sabaghianamir70]

i know ,your right, but take a look to this SRR file . then you see whats im talking about... SRR3474262

[ATpoint]

Look, this method text is just a sumamry from all things they did, so they did RNA-seq and Hi-C but these are independent experiments. They did not do a magical RNA-HiC-seq which is what you seem to think. What you plan to do is not meaningful.