Hi all,

I am attempting to run the dexseqcount.py script using alignedreads.sam and flattened_file.gff as input files.

Unfortunately, I have been receiving the error "line 120 raise SystemError, "illegal strand".

I wanted to ask how to correct this issue.

I have been using the following code:

python dexseqcount.py human_flattened.gff sample1.sam sample1.counts

Thanks.

It means that your strands are outside of the standard '+' and '-' naming convention.

How was your human_flattened.gff file created? Can you show the first few lines from it, please?

Kevin