Get read counts without GTF/GFF files

Question

[weather]

Hi,

I was running some RNAseq for my non-model species, which only have reference genome (FASTA) available in NCBI. Therefore, I was able to run up to hisat2 and get the .bam files.

Normally, I used featurecounts for model species since they will have gft/gff available. I was wondering if there are anyway to get the read counts if gft/gff is unavailable.

Answer 1

[GenoMax]

featureCounts needs to know where the feature boundaries are so it can count the reads. Look into creating a simple annotation format (SAF) as an alternative.

Check subread manual to understand how to create the SAF file.