Jacques Dainat comments

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                                            Jacques Dainat

Combined GeneMark and Augustus gtf conversion issues.

@Lamm-a could you copy pas a chunk of the output file, e.g. 50 lines?

Combined GeneMark and Augustus gtf conversion issues.

Ok here is the full record of the first example... there is no CDS problem ^^. This is good to know. ``` PseudaA_8021 AUGUSTUS CDS 2 31 0.82 + 0...

Combined GeneMark and Augustus gtf conversion issues.

Yes for what you want to achieve it sounds the best solution

Each line of the file must be less than 65,536 characters

I made a toolkit ([AGAT](https://github.com/NBISweden/AGAT)) and I have several scripts using `Bio::DB::Fasta`. Myself I never use single line fasta files, but I got several time user feedbacks having this error....

Each line of the file must be less than 65,536 characters

I don’t see any obvious way to patch that.

Bio::DB issue on MAC using APFS (ssd hard drive).

Updating to macOS Mojave (10.14 (18A391)) has fixed the issue for me.

Update gaas_create_annotation_project.pl to current work-flow demands

I was... You need to release a new release on GitHub it will automatically bump to bioconda.

Updated the script: 1- moving lines related to moving fasta file from…

I let you merge in case you think about other things you would like to change before.

error in gff file (rnaseq branch test-datasets/reference/genes.gff)

I can provide you a fixed version of this file if you wish

error in gff file (rnaseq branch test-datasets/reference/genes.gff)

We also found an awkward transcript at the end of the file that has a CDS of 3 nucleotides long. ``` I ensembl transcript 224563 224862 . - . ID=YAR070C;Parent=YAR070C;geneID=YAR070C;gene_biotype=protein_coding;gene_name=YAR070C;gene_source=ensembl;gene_version=1;p_id=P48;transcript_biotype=protein_coding;transcript_source=ensembl;transcript_version=1;tss_id=TSS435...