HTSeq-Count settings

[dgorelik]

Hey all,

I was wondering if anyone knew the minimum intersection for a read to be counted in the attached scenario (bottom) in the intersection-nonempty setting, and if there is anyway to change it?



Thank you so much!

[dgorelik]

Does anybody know?

[crazyhottommy]

I assume it is 1 bp. I do not know how to change it...

[dgorelik]

So, that means, for example, if a read begins with A, it will map to any genes that end with A?

That doesn't seem to be very useful...

[jparsons]

It's not quite as bad as you make it out to be, dgorelik: If a read maps to position 1000-1100 (with the specific 100mer sequence which that entails), it will add a count for a gene which ends at position 1000.

HTSeq isn't doing anything with the base content of the read - only the genomic positions to which those reads map.

[dgorelik]

Okay, I understand. Thanks for clearing that up.