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Old 08-15-2013, 08:03 AM   #1
dgorelik
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Default HTSeq-Count settings

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!
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Old 08-16-2013, 08:36 AM   #2
dgorelik
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Does anybody know?
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Old 08-16-2013, 08:48 AM   #3
crazyhottommy
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I assume it is 1 bp. I do not know how to change it...
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Old 08-16-2013, 08:58 AM   #4
dgorelik
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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...
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Old 08-16-2013, 09:15 AM   #5
jparsons
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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.
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Old 08-16-2013, 09:26 AM   #6
dgorelik
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Okay, I understand. Thanks for clearing that up.
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