How to select models for anno

[hmyh1202]

Hello:

How to prepare special defined models to suit custom library type , such as one prepared a standard 15 array element model, or one use new linker primers.

$ longbow model --list-models
[INFO 2021-11-02 15:27:28 model] Invoked via: longbow model --list-models
Longbow includes the following models:
Name Version Description
mas15 1.0.0 The standard MAS-seq 15 array element model.
mas15v2 2.0.0 The standard MAS-seq 15 array element model.
mas15threeP 2.0.0 The 3' kit MAS-seq 15 array element model.
mas15BulkWithIndices 1.0.0 A MAS-seq 15 array element model with a 10 base index just before the 3' adapter for bulk sequencing.
mas10 1.0.0 The MAS-seq 10 array element model.
mas10v2 2.0.0 The MAS-seq 10 array element model.
mas10threeP 2.0.0 The 3' kit MAS-seq 10 array element model.
slide-seq 0.0.1 The Slide-seq 15 array element model.
slide-seqV2 2.0.0 The Slide-seq 15 array element model.
mas8prototype 1.0.0 The prototype MAS-seq 8 array element model.
mas8prototypeV2 2.0.0 The prototype MAS-seq 8 array element model.

Thank you!

[hmyh1202]

And the usage description is different bewteen the README and the Longbow documentation page](https://broadinstitute.github.io/longbow/).

The data process steps is difference, the alignment software is also differ.

[jonn-smith]

You can use longbow model -d <MODEL NAME> to create a .json file that defines a model. You can then modify this json file to contain the information specific to your library. Make sure you change the name first, otherwise longbow may not operate properly.