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alexdobin / STAR

RNA-seq aligner
MIT License
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Visualization of read counting rules #859

Open frenkiboy opened 4 years ago

frenkiboy commented 4 years ago

Dear Alex,

Would it be possible to include in the next iteration of the manual, a visualization of how STAR counts reads with regards to read position with respect to one or multiple (overlapping) features? - similar to the famous bedtools figure: https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html

It would be extremely useful if the figure covered different STARsolo counting modes.

Best regards,

Vedran

alexdobin commented 4 years ago

Hi @frenkiboy

if you are asking about the --quantMode GeneCounts option, STAR counting is exactly the same as htseq-count "union", and there is a good picture in their documentation: https://htseq.readthedocs.io/en/release_0.11.1/count.html

For STARsolo Gene counting, it's very similar to the htseq-count intersect_strict option. I should actually make careful comparisons to see if it's exactly the same.

Cheers Alex