# Hisat2 BAM file output does not include stats -- Not a default output but is an option on the tool form **URL:** \ **Category:** usegalaxy.eu support\ **Tags:** mapping\ **Created:** [May 22, 2020, 2:23pm UTC](https://help.galaxyproject.org/t/hisat2-bam-file-output-does-not-include-stats-not-a-default-output-but-is-an-option-on-the-tool-form/3764 "2020-05-22T14:23:57Z")\ **Posts on this page:** 1\ **Showing post:** 2
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [May 22, 2020, 7:04pm UTC](https://help.galaxyproject.org/t/hisat2-bam-file-output-does-not-include-stats-not-a-default-output-but-is-an-option-on-the-tool-form/3764/2 "2020-05-22T19:04:24Z")
Hi @MarioG [https://bam.iobio.io](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](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/3/31fad0bc77ed62993b477df729739e4a6efff752.png) There are also other ways to generate alignment statistics – review tools under the group `SAM/BAM` for the choices available at [usegalaxy.eu](http://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! --- _[View the full topic](https://help.galaxyproject.org/t/hisat2-bam-file-output-does-not-include-stats-not-a-default-output-but-is-an-option-on-the-tool-form/3764)._