trim reads before data processing

[yeroslaviz]

Hi, in the paper in the secrtions about data processing you mention:

Barcode reads were trimmed to exclude the intersub-barcode linear amplification adapters using a mawk script. 

Can you please elaborate on that? what was trimmed?

Is it possible for you to share the script?

thanks

[fderop]

Hello @yeroslaviz,

This concept is explained in detail in the analysis notebooks.

Recently, this is not necessary anymore since our automated pipeline PUMATAC does this automatically.

You can thus reproduce our results with our data by using PUMATAC, which takes care of these steps under the hood.

Florian