AnswerBun.com

if I know the number of sequencing circles can I give this information to DESeq2?

I am trying to understand library normalization in DESeq2. I would like to ask the following: I know that some samples have been run 15 cycles and some others 20, can I give this information to DESeq2, would it be useful? I mean, I know that DESEQ2 uses an algorithm to normalize library size, but since I have this piece of information, I wonder if it would be useful to provide it somehow to DESEQ2. If it is not, would it make sense to incorporate this information in the design matrix, something like: design(~cycle+condition)? Thank you a lot!

Bioinformatics Asked by marilu on January 2, 2021

1 Answers

One Answer

You can include that info in the design, though you'd have to decide whether to include it as a number of just a factor. I've never heard of anyone including PCR cycles. I've heard of people including RIN scores, though I've never done it.

If the PCA looks alright, I wouldn't worry about. I've got tons of examples of the lab people saying "I did a few more cycles on these few samples" and then you can't tell any difference in the PCA. I think needing to do more cycles likely has more to do with variance in the prep than a real biological difference.

Answered by swbarnes2 on January 2, 2021

Add your own answers!

Related Questions

Block wise protein imputation

2  Asked on March 23, 2021 by whateversclever

     

RAD Seq Data Analysis without barcode

2  Asked on March 20, 2021 by biobash

   

FASTA and PDB: How to specify chain?

2  Asked on March 19, 2021 by lazer-guided-lazerbeam

     

How can I use my Myheritage DNA results file for further analysis?

1  Asked on March 19, 2021 by user3390486

   

Within and between sample count normalization

1  Asked on March 16, 2021 by maxno3

     

Too slow issue of BioMart

1  Asked on March 12, 2021 by user224050

   

Obtaining Whole Genetic Sequence

2  Asked on March 11, 2021

     

Ask a Question

Get help from others!

© 2022 AnswerBun.com. All rights reserved.