Hisat2 BAM file output does not include stats -- Not a default output but is an option on the tool form

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Hi @MarioG

https://bam.iobio.io is a nice graphical summary tool for BAM/SAM alignment stats.

To output statistics directly from HISAT2, that output option needs to be set to “Yes” on the tool form. Find it nested under the section “Summary Options”. This would allow you to use MultiQC to compare multiple BAM results together in a single report.

hisat2-output-alignment-stats
hisat2-output-alignment-stats1466×370 30.4 KB

There are also other ways to generate alignment statistics – review tools under the group SAM/BAM for the choices available at usegalaxy.eu.

If you plan to go forward with differential expression analysis, after generating counts (example: Featurecounts or HT-seq count), those results can be examined with scientific content metrics with the tool QualiMap Counts QC.

Thanks!

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