# featurecounts error using BAM and gff3 files

**URL:** <https://help.galaxyproject.org/t/featurecounts-error-using-bam-and-gff3-files/8908>\
**Category:** usegalaxy.eu support\
**Tags:** transcriptomics\
**Created:** [October 26, 2022, 7:03pm UTC](https://help.galaxyproject.org/t/featurecounts-error-using-bam-and-gff3-files/8908 "2022-10-26T19:03:17Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![Luisa\_Nieto](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/luisa_nieto/32/3753_2.png) [@Luisa\_Nieto](https://help.galaxyproject.org/u/Luisa_Nieto)\
**Post date:** [October 26, 2022, 7:03pm UTC](https://help.galaxyproject.org/t/featurecounts-error-using-bam-and-gff3-files/8908/1 "2022-10-26T19:03:17Z")

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Hi. I am having this error, using the featurecounts tool:  
An error occurred with this dataset:  
format tabular database  
========== \_\_\_\_\_ \_ \_ \_\_\_\_ \_\_\_\_\_ \_\_\_\_\_\_ \_\_\_\_\_ ===== / \_\_**| | | | \_ | \_\_ | _| /\ | \_\_ \ ===== | ( | | | | |_) | |) | | / \ | | | | ==== \_** | | |  
The input was a file with mapped reads in BAM format and a gff3 file from my reference genome.

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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 26, 2022, 9:56pm UTC](https://help.galaxyproject.org/t/featurecounts-error-using-bam-and-gff3-files/8908/2 "2022-10-26T21:56:12Z")

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Hi @Luisa_Nieto

Let’s please continue in your original topic. Please try the advice given first. It solves most if not all technical errors. Scientific content problems are different but you can’t troubleshoot those until the technical are resolved.

Be aware that GFF3 doesn’t always work well – GTF always does when the formatting is right. If you want to share a link to your history, that would help. Post that back into a reply in that topic please. If you’d rather not post that publicly, ask for a moderator to start up a private message chat to use instead.

> [@new annotated bacterial genome](https://help.galaxyproject.org/t/new-annotated-bacterial-genome/8894/4):
>
> Hi @Luisa_Nieto Thanks for explaining slight_smile Use a custom genome fasta and optionally promote that to a custom build to create a “database” metadata that be assigned to datasets. Some tools use the fasta directly and some tools require/use the “database” metadata. Tip: avoid assigning an existing “database” to any data that is associated with a custom genome fasta – instead create your own custom database key to avoid content conflicts that can be difficult to interpret. The general f…

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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 26, 2022, 9:56pm UTC](https://help.galaxyproject.org/t/featurecounts-error-using-bam-and-gff3-files/8908/3 "2022-10-26T21:56:19Z")

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Closed on October 26, 2022, 9:56pm UTC