Unfortunately, don't. But I think If you've PairEnd data you could safetly remove PCR duplicates. However, I neved did it for SOLiD.
About "base reclaibration" I'm going to try it. I'm waiting for finishing alignment step to try it. I'll let you know then.
By other hand, I'm using BFAST to align to colospace but it is extremely slow. What alignerare you using?
-
Actually I also have similar doubts (though working with paired data). Do you have any progress or hints on this topic?Leave a comment:
-
Doubts about GATK "raw data processing" step for SOliD exome data
Hello,
I just received SOLiD 75bp fragment (SE) exome data. I haven't previosly worked with SOLiD data and I'm not sure the suitable way to handle them for a further GATK based variant detection. In concrete I have doubts about:
- filtering PCR duplicated
I'm undecided to filter or not them using picard markduplicates. Being SingleEnd data I'm inclined not to do it to avoid lose "true" reads (not duplicates) at expense of generate "dirty" variant calls. What's you opinion?.
- base recalibration
Due to special caracteristics of colorspace read seems to be unnecessary to make base recalibration. I checked "1000 Genomes" paper (http://www.nature.com/nature/journal...ture09534.html) where based recalibration was avoided for SOLiD data. By other hand, in GATK documentation (http://www.broadinstitute.org/gsa/wi..._recalibration) "PrimerRoundCovariate" covariate is described as "The primer round for this base (only meaningful for SOLiD reads).". I'm confused and do not know if the recalibration of bases is a recommended step for SOLiD.
Any advice?
I would appreciate your help.
Thank you
-
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.
Methylation Detect...05-31-2023, 10:46 AM -
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
Leave a comment: