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Well, the minimum number would be 2, but you'll want to merge all of the samples involved in any comparison that you intend to make. -
Transcriptome Assembly Questions for Cuffmerge
Hi. I am trying to run a rather large experiment for my first RNAseq project. Unfortunately, I was convinced to use our SOLiD machines due to cost and proximity (but that's a different issue
). Let's say I get past this and have some mapped reads to input into Cufflinks and then Cuffmerge to make an assembly.
How many Assembled Transcripts from how many replicate samples are required as input to Cuffmerge to make the final assembly? Do I need to dump ALL of the Assembled Transcripts for each experiment?
The experiment is using three genotypes (Control, Del, Dup) and three biological replicates per genotype (R1, R2, R3). In addition, we are using both DPSCs and DPSC-neurons for all of these conditions. I said it was big!
Any help appreciated.
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Developments in sequencing technologies and methodologies have transformed the field of epigenetics, giving researchers a better way to understand the complex world of gene regulation and heritable modifications. This article explores some of the diverse sequencing methods employed in the study of epigenetics, ranging from classic techniques to cutting-edge innovations while providing a brief overview of their processes, applications, and advances.
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Differential Expression and Data Visualization: Recommended Tools for Next-Level Sequencing Analysis
After covering QC and alignment tools in the first segment and variant analysis and genome assembly in the second segment, we’re wrapping up with a discussion about tools for differential gene expression analysis and data visualization. In this article, we include recommendations from the following experts: Dr. Mark Ziemann, Senior Lecturer in Biotechnology and Bioinformatics, Deakin University; Dr. Medhat Mahmoud Postdoctoral Research Fellow at Baylor College of Medicine;...05-23-2023, 12:26 PM -
Continuing from our previous article, we share variant analysis and genome assembly tools recommended by our experts Dr. Medhat Mahmoud, Postdoctoral Research Fellow at Baylor College of Medicine, and Dr. Ming "Tommy" Tang, Director of Computational Biology at Immunitas and author of From Cell Line to Command Line.
Variant detection and analysis tools
Mahmoud classifies variant detection work into two main groups: short variants (<50...05-19-2023, 10:03 AM
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