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
-
Tumors contain complex mixtures of cell populations that evolve in response to treatment and host-specific factors. Tissue biopsies provide only static snapshots of a tumor’s state. But what if we could follow that evolution over time using a minimally invasive technique?
Liquid biopsies can detect tumor-derived material circulating in the bloodstream, providing a way to study treatment response, detect emerging resistance, and discover new biomarkers. Circulating...10-14-2026, 09:55 AM -
Researchers using sequencing and genomics tools often have to make trade-offs. They can choose between speed or scale, short reads or long-range information, or targeted panels or a view of the whole transcriptome. New technologies that have been released this year are built to address those tough choices.
We asked six companies the same four questions to learn about their latest products. The new technologies bring a lot to the table, including rethinking sequencing...
Comment