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We did some PCR sequencing on Miseq and are trying to see if we could use a stringed together sequence of all amplicons to creat a pseudogenome and input for Miseq reporter in the resequencing option. As we have some internal barcodes in the products, each of our amplicons would have replicates with the different tags at each end. Anyone else has done something similar?
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It should work in theory, but I don't know if the inline barcodes will mess anything up in MSR.You can just try it and report back the results. All you have to do is upload a FASTA file in MCS, then use assign your samples to use it as the genome in MSR. You can requeue the analysis as many times as you want until you get things working just right. -
It does work! Now the next step would be to see if an annotation file can be created for the pseudo genome so that the Miseq reporter can put out the results with annotation. The annotation would be the identity. Could anyone shed some light on how to annotate a psedogenome...Comment
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Is the fasta header not informative enough? You could also make a bed file that contains the identity information.Comment
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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...Yesterday, 07:01 AM -
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...04-04-2024, 04:25 PM
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