In the tutorial it is suggested that we include a second factor “sequencing”: and include paired and unpaired count files. My question is if all my read files are paired, is there a need to do this step in DeSeq2? GalaxyProject tutorial , Time point: 4:01 - shows that they have both paired and unpa…

Hi @Sanjukta_Ghosh factors are determined by nature of your experiment. If all samples were sequenced on the same platform and groups nicely cluster together on PCA plot, you probably don’t need additional factor. Maybe check this tutorial for more information: Transcriptomics / Hands-on…

Is there a need to include 2nd factor if there's only paired reads in the dataset for DeSeq2?

usegalaxy.org support

jennaj February 21, 2024, 5:20pm 4

Conversation continues at Help needed in PCA plot analysis

Topic		Replies	Views
Problem in DESe2 with multiple factors usegalaxy.eu support transcriptomics , rna-seq , deseq2	3	210	October 24, 2023
error when using several factors in deseq2 usegalaxy.org support	0	437	December 2, 2020
DESeq2 with pair end file (Stringtie) usegalaxy.org support transcriptomics , rna-seq , deseq2 , stringtie	1	205	September 5, 2023
Deseq2 Biological v. Sequencing replicates	0	323	March 4, 2021
RUVseq in usegalaxy.org usegalaxy.org support	2	625	March 2, 2020

Is there a need to include 2nd factor if there's only paired reads in the dataset for DeSeq2?

Related topics