Best practice specifying library type for 10X data

[TereLaguinge]

Hi,

I'm working on analyzing some 10X Chromium V2 5' data using Salmon Alevin and Alevin Fry. I've been looking up on several issue to figure out what library type (-l) and expected orientation (--expected_ori) to use for my data.

I've looked out several other issues regarding 5' data:

• Issue 118
• Issue 439

The documentation ( Alevin Fry Documentation ) seems to recommend you using ISR as library type for 10X v2 data but from the issues it seems like people are divided in using ISR or ISF.

From Salmon documentation on library type ( Salmon Documentation ) seems like we should be using ISF for 5' 10X data.

I would like to know if there are any specified best practices for which library type and expected ori to use for this type of data. Could someone explain what is the biological meaning of this?

Best,

Teresita