Dear colleagues, I am a new Galaxy user motivated to exploit its tools to compare two sets of the data from transcriptome sequencing of an extremophilic fungus Acidothrix acidophila. The genome and transcriptomes of the fungus have been sequenced by JGI within the frame of the 100 Fungal genomes project. As a result, I received fasta files of genome and fasta files of genes (Gene catalog of transcripts, gene catalog of proteins (both for best models and all models), as well as the corresponding GFF and GFF3 files. In Galaxy, after grooming, I mapped both transcripts against the Gene catalog fasta file using BWA-MEM, received BAM files and tried them use to get transcript counts using Htseq-count with with gff as well as gff3. At this point, however, I received error messages :
"Fatal error: Unknown error occured Error occured when processing GFF file (line 5 of file /galaxy-repl/main/files/015/198/dataset_15198690.dat): Feature exon_1_1 does not contain a 'gene_id' attribute [Exception type: ValueError, raised in count.py:53]"
The option "Autodetect" did not solved the problem. It seems to mee that the input data provided are not meeting the demands of galaxy tools and may be, I did some basic error(s) which I do not understand, and the gff/gff3 file lacks important data..
I would be grateful to you for any advice how to proceed further in simple comparison of two transcriptomes. My user name is gryndler@biomed.cas.cz and i have just one (unnamed) history.
Thank you in advance for any response
Milan Gryndler
gryndler@biomed.cas.cz
