HISAT2 - Could not display BAM file

5

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?

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. 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.

    • Try running FastQC to see if it was fully uploaded. If that tool fails, the dataset was likely truncated upon Upload. Loading again is usually how to fix that type of problem. It doesn’t seem like that original dataset is truncated, if it worked at usegalaxy.org. Be sure to use “autodetect” for the datatype assignment.

FAQs: https://galaxyproject.org/support/

Thanks!