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We use fastq_dump to convert the downloaded .sra files to fastq. When the data is single-ended, only one output file is created: Run_XXX.fastq. When the data is pair-ended, the dump usually creates two output files: Run_XXX_1.fastq and Run_XXX_2.fastq, for the paired reads (forward in _1, reverse in _2). Sometimes it creates a third output file, Run_XXX.fastq, where it puts reads that are in the raw data, without their paired read. Normally when this happens, the third file is very small compared to the paired files, and I discard it, but in the current experiment the third file is half the size of each of the paired files. What do you think should I do with a rna-seq run that its fastq dump has a lot of unpaired reads (half the number of the pairs)?
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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
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