Hi

I'm uncertain about what parameters I'm supposed to feed to FeatureCount.
I have a BAM-file and a GFF file (from Prokka).
The GFF-file looks like this:

```
003__g__Streptococcus_no_23	Prodigal:2.6	CDS	6098	6310	.	-	0	ID=PLMABFGE_03080;inference=ab initio prediction:Prodigal:2.6;locus_tag=PLMABFGE_03080;product=hypothetical protein
003__g__Streptococcus_no_23	Prodigal:2.6	CDS	6340	6504	.	-	0	ID=PLMABFGE_03081;inference=ab initio prediction:Prodigal:2.6;locus_tag=PLMABFGE_03081;product=hypothetical protein
003__g__Streptococcus_no_23	Prodigal:2.6	CDS	6641	7483	.	+	0	ID=PLMABFGE_03082;Name=ykuT;db_xref=COG:COG0668;gene=ykuT;inference=ab initio prediction:Prodigal:2.6,similar to AA sequence:UniProtKB:O34897;locus_tag=PLMABFGE_03082;product=putative MscS family protein YkuT
003__g__Streptococcus_no_23	Prodigal:2.6	CDS	7514	8083	.	-	0	ID=PLMABFGE_03083;inference=ab initio prediction:Prodigal:2.6,similar to AA sequence:UniProtKB:P39157;locus_tag=PLMABFGE_03083;note=UPF0340 protein YwlG;product=hypothetical protein
003__g__Streptococcus_no_23	Prodigal:2.6	CDS	8115	8582	.	-	0	ID=PLMABFGE_03084;Name=hmpT_2;db_xref=COG:COG4720;gene=hmpT_2;inference=ab initio prediction:Prodigal:2.6,similar to AA sequence:UniProtKB:A2RIH3;locus_tag=PLMABFGE_03084;product=Thiamine precursor transporter HmpT
```
The BAM-file is an alignment of my raw FASTQ-files (from a metagenomic sample) mapped against the genes predicted from my assembled bins.
The purpose is to figure out, how many reads are mapped to each gene (the depth/abundance of each gene) and lastly, cluster them together in COGs or some sort of functional categorization.

What should I set my -t and -g values to?
I found the issue. I was using an alignment of the genes rather than the chromosomes, hence the confusion.
I made a new alignment, and everything looks good now!