Definition of numReadsLongestSub

[sum732]

Hello Developers,

Thanks for creating the SequelTools.

Just a basic question, how is numReadsLongestSub defined. I tried to look in to the scripts to identity the cuotff, but could not find it out. Are these reads above a certain length, if so how is this decided? If so such hard limits then how is a LongestSub defined?

Thanks, Deep

[DavidEHufnagel]

Hello,

Thank you for your interest in SequelTools and my apologies for the late reply.

numReadsLongestSub is simply the number of longest subreads for a given SMRTcell, where longest subreads are defined as the longest subread in a CLR. So for any template the polymerase will attempt to read it and hopefully will read the subread multiple times. When that works out this produces multiple subreads for one CLR. SequelTools identifies one of those subreads as the longest one. In the case where something like 1.5 or 2.5 subreads are read, which is fairly common, it is very useful to know which is longer and use that one. In some cases multiple subreads have the same exact length in which case SequelTools will choose one randomly to be the longest subread.

Best, David E. Hufnagel

On Wed, Feb 17, 2021 at 12:59 PM sum732 notifications@github.com wrote:

Hello Developers,

Thanks for creating the SequelTools.

Just a basic question, how is numReadsLongestSub defined. I tried to look in to the scripts to identity the cuotff, but could not find it out. Are these reads above a certain length, if so how is this decided? If so such hard limits then how is a LongestSub defined?

Thanks, Deep

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