Tweet
Hi all, I am using HISAT2 and trying to write unmapped reads from paired-end data and the flag --un is resulting in empty files. I know they are not all mapping so does anyone have any recommendations to write those reads to a file?
-
-
Hi I had the same problem, you need to use --un-conc for paired end reads (write paired-end reads that fail to align concordantly to file(s) at <path>). There is an explanation of the relevant SAM flags in the help manual for Hisat2. -
Thanks for the reply! I was hoping there was a means of writing out only those mates that did not map anywhere rather than all reads that did not map concordantly, but it is a good place to start I suppose.Comment
-
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 on Modified Bases...Today, 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
Comment