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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...
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Thanks NextGenSeq. That is exactly what I'm looking for but I guess not in a commercial package
Originally posted by NextGenSeq View PostProbably 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.
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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.
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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.
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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.Tags: None
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The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...-
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Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...-
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