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How about Newbler for the 454 reads? Not sure how it would deal w/ PacBio data, but if you use fasta + qual I think it could handle it (depending on read length).
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I guess it depends on how many reads you've got. For a moderate number of seuqences BLAT does a good job as well.
I used bwasw for 454 data as well and it worked out nicely.
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454: Extremely general question
All,
I have 454 and PacBio SRA data (that are cleaned of adaptors) that I'd like to align to a reference. I've tried bwasw, but when I look at the alignments in samtools tview, they are rather subpar as compared to data that has been reported by others on these sequences. Any suggestions for general approaches to aligning long reads? bwasw should work, correct? Better tools for dealing with these data?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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04-22-2024, 07:01 AM -
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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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