Why does my GTF file not convert into a BED12 file with the GTF to BED12 converter tool?

[Coral]

I am analyzing human RNA-seq data with galaxy. To map reads I am using the latest version of the human Assembly GRCh38.p14, which I downloaded with this name (GCF_000001405.40) from this website (Homo sapiens genome assembly GRCh38.p14 - NCBI - NLM) and even though I can map reads with this gtf fileu sing RNASTAR when I view the read distribution I cannot transform this file to a bed12 file with the converter tool (GTF to BED12). Even though I can transform the file into a BED file, the Read Distribution tool only works with BED12 files.
Is there any other tool I can use to analyze read distribution?
Is there a way to transform my gtf file to a bed12 format without receiving an error message?

Thank you very much in advance,

Coral

[jennaj]

Welcome, @Coral

If you are getting an error message, we can try to solve that here.

The GTF choice from there would be the best file. If you were using a different file, try this one instead.

• Source directory → Index of /genomes/all/GCF/000/001/405/GCF_000001405.40_GRCh38.p14
• File → https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.40_GRCh38.p14/GCF_000001405.40_GRCh38.p14_genomic.gtf.gz

Paste the URL into the Upload tool using all defaults. The data will be uncompressed and assigned the datatype gtf.

Next, check for headers. Why? Many tools (in Galaxy or not) will complain since those # lines are technically out of specification for “strict GTF format”.

• Format spec (same other places, so this is just an example) → Genome Browser FAQ
• Our guide about the format, plus help with removing any data provenance headers → FAQ: Working with GFF GFT GTF2 GFF3 reference annotation

This should definitely work but you can share back your issue in a history for feedback. Without seeing the error, input data, and tool/options is is hard to guess what else might be going wrong. → How to get faster help with your question