I am unable to assign the correct attributes to my gtf file to use with featurecounts tool. The overall alignment rate is 95.61%, so there is no problem with mapping using bowtie2. While trying to use featurecount, I get the following error:
> ERROR: no features were loaded in format GTF. The annotation format can be specified by the ‘-F’ option, and the required feature type can be specified by the ‘-t’ option.
> The porgram has to terminate.
I annotated the genome using RAST, and uploaded the gtf file from my PC. Since I am using a custom genome, I did the custom build and assigned the genome to both gtf and bam inputs. I am sure there is a problem with identifiers in the genome, bam, and file but I don’t know how do I make identifiers the same. Is there a tool that is used for this problem. Can someone please suggest a solution. I am running short on time and would appreciate any help. I can share my galaxy workflow if someone needs to look at it. Thank you