Collect all the single full length LTR elements before the "building examplars" step

[uceleste]

Hi All,

I'm using the Repeats pipeline and I know that it produces representative sequences (examplars).

However, I'd like to have also the dataset with all the single full length LTR elements, so the elements as they are before the "building examplars" step. Which one is the file corresponding to this dataset? passed_outinner_sequence.fasta? lLTRs_Seq_For_BLAST.fasta?

Thank you very much

[willibry]

Hi @uceleste,

I apologize for the late response.

This part of the pipeline follows the instructions found here and I believe it has been updated since I made this pipeline. I recommend you follow the guidelines there.

The files you mention contains the long terminal repeats and inner sequence in separate files. I think the CRL_Step3_Passed_Elements.fasta should contain the whole sequences before the "building examplars" step.

Best regards,

William