I have about 12 samples I aligned with mm39. All samples had good quality reads and all paired, as trimmomatic gave me empty files for unpaired reads. Strangely, two of them had 0% alignment with the genome. I blasted a few reads and they seem to match mus musculus or other rodents. I’m using HISAT2…

Hi @Diogo_de_Moraes1 Try a rerun with the data that didn’t align, just to eliminate server/cluster issues from being a factor. As you do that, double-check that the correct target reference genome is selected on the tool form. The most current version of the mouse genome is GRCm38 (mm10, sourced f…

HISAT2 reports samples with 0% alignment rates

usegalaxy.org support

jennaj Split this topic September 23, 2022, 10:02pm 5

A post was split to a new topic: Can I use data based on different genome assemblies?

Topic		Replies	Views
Low HISAT2 alignment rate and low featurecounts assigned rate usegalaxy.org.au support transcriptomics	1	223	April 23, 2024
Problems mapping with HISAT2 & BOWTIE2 usegalaxy.org support mapping	4	2843	February 28, 2019
HISAT2 Virus Alignment Settings mapping , single-cell	2	570	October 28, 2021
In featurecounts I got 69% assigned but count matrix full of zeros usegalaxy.org support usegalaxyorg , gtn-tutorial , htseq-count , reference-genome	4	615	November 4, 2021
Error with HISAT2 usegalaxy.org support transcriptomics	3	11	April 3, 2025

HISAT2 reports samples with 0% alignment rates

Related topics