Hi Bruce,
I would suggest you trying to count reads instead of fragments to see if you will still get a large number of reads overlapping with multiple genes. This will help determine if the large number of multi-overlapping fragments you observed were due to summarization.
If you still get a large number, then that will mean it is either a mapping problem, or a problem with your data generation, or a lot of genes in your annotation overlapping with each other.
You can simply remove those paired-end parameters, such as -p -P -D and -C, from your command to summarize reads instead of fragments.
Best wishes,
Wei
I would suggest you trying to count reads instead of fragments to see if you will still get a large number of reads overlapping with multiple genes. This will help determine if the large number of multi-overlapping fragments you observed were due to summarization.
If you still get a large number, then that will mean it is either a mapping problem, or a problem with your data generation, or a lot of genes in your annotation overlapping with each other.
You can simply remove those paired-end parameters, such as -p -P -D and -C, from your command to summarize reads instead of fragments.
Best wishes,
Wei
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