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Are you willing to do a bit of programming? You can view the BAM file in SAM format (see the manual), send the output to a file, run a program to decode the colorspace bits, and then go from there... -
Probably not want you are looking for since it's commercial but CLCBio's Genomic Workbench shows the basepair detail, original color space call and quality values in the alignment contigs.Leave a comment:
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I've been using IGV all this time. It works fine although what I mean is that I would like to be able to view the actual base-pair detail at the highest resolution.
Perhaps it is the structure of my BAM file but I guess I will need to consult the IGV support team if it is an issue.Leave a comment:
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You can open the sorted BAM file in IGV (http://www.broadinstitute.org/igv/)Leave a comment:
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Colorspace alignment visualization
Hi Community,
I am not entirely satisfied with what's available for whole-genome browsing of color space alignments.
I have tried IGV and had a look at the SOLiD alignment browser but I have run into some problems
I have a sorted BAM file from BFAST and I'm not sure how to change this to the Bioscope GFF3 format.
Has anybody had better luck in properly displaying colorspace alignments to a reference genome? I would like to see SNPs, sequencing errors, etc. in colorspace as compared to the reference sequence.
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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.
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
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