# HISAT2 - Could not display BAM file

**URL:** <https://help.galaxyproject.org/t/hisat2-could-not-display-bam-file/2303>\
**Category:** Uncategorized\
**Tags:** fastq-format\
**Created:** [October 18, 2019, 10:20am UTC](https://help.galaxyproject.org/t/hisat2-could-not-display-bam-file/2303 "2019-10-18T10:20:01Z")\
**Posts on this page:** 1\
**Showing post:** 5

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**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:** [October 21, 2019, 4:16pm UTC](https://help.galaxyproject.org/t/hisat2-could-not-display-bam-file/2303/5 "2019-10-21T16:16:01Z")

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Thanks for the clarification about your Galaxy, @artem

So you have tested in both a GVL cloud Galaxy instance and a `19.05` local version of Galaxy, same problem (job errors)? But the same job works at the public Galaxy server [https://usegalaxy.org](https://usegalaxy.org)?

One of these could be going wrong:

1. The genome was not fully indexed. Any genome should have Data Managers run in this order: [Indexing reference genomes with Data Managers: Resources, tutorials, troubleshooting](https://help.galaxyproject.org/t/indexing-reference-genomes-with-data-managers-resources-tutorials-troubleshooting/1223/2). The cloud version of Galaxy would have this genome already indexed. In a local Galaxy, you’ll need to do the indexing.

2. Your data is in `fastqsanger` format and the first read has an exact human genome match (hg19, hg38), so the problem doesn’t seem to be with either of those – unless you manually assigned the datatype to be `fastqsanger.gz` (compressed fastq). When the assigned datatype is a mismatch for the actual data content, errors are produced.

FAQs: [https://galaxyproject.org/support/](https://galaxyproject.org/support/)

- [How to format fastq data for tools that require .fastqsanger format?](https://galaxyproject.org/support/fastqsanger/)
- [Understanding compressed fastq data (fastq.gz)](https://galaxyproject.org/support/compressed-fastq/)
- [Common datatypes explained](https://galaxyproject.org/learn/datatypes/)

Thanks!

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