Raw read count of Treated Vs Untreated

Question

[monikakumar2017]

Hi friends, i am new in RNA-Seq data analysis. When i see the data of total raw reads for the treated and untreated samples usually the untreated samples contain more number of reads than the treated ones. What could be the possible reason? I was expecting to get more reads on the treated but that was not the case. Detailed explanations are appreciated. Thank you

[John]

Just to be sure - you're getting the read count from a FASTQ file right?

[monikakumar2017]

No. Those are derived after aligning the reads back to the reference genome (mapped reads)

[GenoMax]

Then "raw" is not the right word to use. That generally means original sequence data.

untreated samples contain more number of reads than the treated ones

Can you quantify "more"?

[monikakumar2017]

I got 32,295, 321 reads for the treated and 38,512, 390 reads for the untreated

[GenoMax]

Most analysis packages will take these types of differences into account. You should go ahead with DE analysis.

Answer 1

[GenoMax]

There should be no direct correlation between number of reads and underlying experimental condition (or it would be hard to find one, even if you start with equimolar amounts of input material).

Number of reads you obtain from samples are dependent on quality of input material/quality of libraries that got made/amount of library loaded on sequencer and overall metrics of the run.