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We are working with a novel plant transcriptome (no reference genome). After annotating the assembly, will removing irrelevant contigs effect read mapping statistics, in a good way, when we perform RNA-Seq analysis? Many of our contigs annotate as retrotransposons, bacterial/viral contaminants (metagenomic leftovers), or have no match to any annotated proteins in public databases. I assume contaminants should be removed, but what about genes of no interest to our research (e.g. transposable elements)? Will our results be more accurate if the our transcriptome only contains known and relevant protein coding contigs?
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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...04-04-2024, 04:25 PM -
Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...03-22-2024, 06:39 AM