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I have done an alignment and used the -H option to dump the multiple hits as well as the -u option to dump the reads that do not map. However, after the alignment, I was interested in getting the numbers of hits in each category (# unique mapping reads, # reads that map to multiple places, and # reads that do not map). I converted the 'map' file to a 'txt' file and counted the number of lines (I got 8,335,894) and then I counted the lines in the non-mapping file (I got 4,575,039). However, this totals to the total number of reads that I started with (12,910,933)! What goes in the multi mapping file? I unzipped it, but cannot discern the format at all. Do the reads that map to multiple positions also go on the 'map' file?
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The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...05-06-2024, 07:48 AM -
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...04-22-2024, 07:01 AM