metadata file and soft masking

[ardy20]

Could you please explain how to prepare metadata file and which tool is suggested for soft masking of the genome?

[sagnikbanerjee15]

Hello @ardy20,

Please follow the sample metadata as provided in the example. Essentially, you need to provide either an SRA number or the location on the hard disk from where the raw data could be accessed. For soft-masking, you can use repeatmasker. The new version of the pipeline will have a tool built-in to perform repeat masking.

Thank you.

[ardy20]

Do you have any plan to include repeat modeller?

[sagnikbanerjee15]

Hello @ardy20,

Sure I can include repeat modeller.

Thank you.

[DrDoom-EvoGen]

Has repeat masking been added to the newest version of FINDER?

[sagnikbanerjee15]

Hello @DrDoom-EvoGen,

Thanks for your patience. We have repeat masking implemented as a module but have not yet integrated it into the pipeline.

Thank you.