What's the meaning of "not_alignment" from the output of HTseq-count? The manual says it is the "reads in the Sam/Bam file without alignment". Does this mean the reads that are not mapped to the reference? or anything else? Thanks!
-
-
Yeah, these are just reads that didn't align. Whether the count for this is 0 or not will depend on the aligner that you're using (some don't put unaligned reads in the output SAM/BAM file, others do). -
Assuming that the file I used for input of HTseq-count includes the unaligned reads in the output BAM file, But the number of "no_alignment" reads doesn't match the number of reads not mapped to the reference. Any idea about this? Thanks!Comment
-
it should match. Maybe it's paired-end? (htseq-count counts read pairs, not reads)Comment
-
@flyingoyster: Try using the -o option to see what's going on in your case.Comment
-
@Simon Anders, Yes, My data is paired-end. If HTseq-count counts read pairs, not reads, that makes sense. Thanks a lot!
@dpryan, I used Galaxy server, so not be able to choose options.
If I want to calculate the number of reads within genes, is it right to substract the number of no_feature reads from the total number of mapped reads? Thanks!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