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Hello,
I have a question regarding the purpose of the size selection.
Apart from the more obvious reason to exclude adapter/primer dimers, the mapping of paired-end data requires a defined insert size.
Now my question:
Is it preferable to select the fragment-size as narrow as possible (which could make the mapping of paired-end data more accurate, but might lead to the loss of some information!?)
OR
would you select a rather broader range (which might allow the identification of more splice-sites, see also https://www.landesbioscience.com/jou...ache=967631737).
Maybe the mapping works just as fine with a broader range as long as you know and can provide the fragment length distribution!?
To me it always seems like a trade-off between the two but I don't know what's state-of-the art...
Since we have the Pippin prep in our lab I have the opportunity to select for a size as narrow as +/-8% but I'm not sure this is desirable...
Thanks for your help in advance!
I have a question regarding the purpose of the size selection.
Apart from the more obvious reason to exclude adapter/primer dimers, the mapping of paired-end data requires a defined insert size.
Now my question:
Is it preferable to select the fragment-size as narrow as possible (which could make the mapping of paired-end data more accurate, but might lead to the loss of some information!?)
OR
would you select a rather broader range (which might allow the identification of more splice-sites, see also https://www.landesbioscience.com/jou...ache=967631737).
Maybe the mapping works just as fine with a broader range as long as you know and can provide the fragment length distribution!?
To me it always seems like a trade-off between the two but I don't know what's state-of-the art...
Since we have the Pippin prep in our lab I have the opportunity to select for a size as narrow as +/-8% but I'm not sure this is desirable...
Thanks for your help in advance!