Handling of read abundance

[MikeAxtell]

Hello again Bao. I have another question .. how does SEED incorporate read abundance when determining a representative sequence? For instance, let's say I have a cluster with 10 different sequences. One of these sequences is present at 1,000 reads, while the other nine sequences are present only once in the data. Do all ten sequences count 'equally' in terms of determining the representative sequence? Or is the determination of the representative weighted by abundance (in which case we'd expect the 1,000-read sequence to be the representative in my example).

Thanks again!

[baoe]

Hi, Mike,

We consider single reads, so in this scenario, we have 1000+9 reads instead of 10.

Best,
Bao

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From: Mike Axtell [notifications@github.com]
Sent: Friday, June 10, 2016 11:33 AM
To: baoe/SEED
Subject: [baoe/SEED] Handling of read abundance (#3)

Hello again Bao. I have another question .. how does SEED incorporate read abundance when determining a representative sequence? For instance, let's say I have a cluster with 10 different sequences. One of these sequences is present at 1,000 reads, while the other nine sequences are present only once in the data. Do all ten sequences count 'equally' in terms of determining the representative sequence? Or is the determination of the representative weighted by abundance (in which case we'd expect the 1,000-read sequence to be the representative in my example).

Thanks again!

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