genbank to GTF in galaxy

Question

[basuanubhav]

Hi all, I am working on galaxy and have a genome file in genbank format. To use featurecounts for my RNAseq, I need to convert the genbank format to a GTF format because that's the format the featurecounts tool in galaxy expects. Now, I tried to convert the genbank to GFF3 using GenbaktoGFF3 tool in galaxy and managed the o do so. Also I tried to use the gffread tool to convert the GFF3 file to GTF but this resulted in a GTF with no written line and I can't understand why.

Is there a way to directly convert genbank to GTF in galaxy (or even outside galaxy, but preferably in galaxy). Also, any idea why gffread is not working properly in my case? I am using default parameters (leaving everything as is) and only giving GTF as feature file output and track name as "word".

Thanks,

[cpad0112]

what's the reference organism? you can follow this thread: https://help.galaxyproject.org/t/genbank-to-gtf-for-featurecounts/5283

[basuanubhav]

So the organism is Bacteroides thetaiotaomicron VPI-5482 but the sequence I am supposed to use is the not the sequence you get from Ensembl. I have a specific genbank file that I am supposed to use.

[vkkodali_ncbi]

Did you try using GFF3 file directly with featureCounts? User manual says that one can use GTF or GFF files.

[basuanubhav]

Yes, the manual does say so and I tried it on galaxy using the gff3 file but it didn't work. All my genes had 0 reads so the software must have been having trouble with the format. I think the software they use in galaxy can only use GTF files with the command line version may be able to use gff3. I could use the command line tool but it would mean having to download all the BAM files which I want to avoid.

[cpad0112]

please post example lines from gff3, reference chromosome/contig names and the function you have used in extracting read counts. If gff3 doesn't work, try converting it to gtf (via gffread tool) and try with gtf file.

[cpad0112]

If you are the admin on galaxy, try installing fml_gff3togtf repo from tool shed. It has a tool named fml_gbk2gff. See if that helps you.

[basuanubhav]

Sadly I am not an admin there just an user :(

[cpad0112]

Request the admin to use it. or download the gb and upload it to any galaxy public server with fml_gbk2gff and convert gb to gff file.. Download the history (for future reference) and down the load the gff and upload gff it to your local server. You can also publish your workflow (on public server) and import it into your local galaxy server, if it allows importing from pubic histories.