almeidasilvaf / doubletrouble Goto Github PK

Hi, Is there any quicky tutorial of doubletrouble for finding gene duplication?

Hi again,

When I try the pdata <- process_input(seq,annotation) command, I got the error like this:

Error in check_list_names(seq, annotation) :
Names of list elements in 'seq' and 'annotation' must match.

For protein seq and annotation files, I used the Augustus tool for this sample.

Do you have any suggestions to help me resolve this issue? Thank you for your time.

Best regards

Hi,
I am having trouble with the input file format and despite following the tutorials you provided, the output file remains empty like this:

This file is a protein fasta file like this:

I have tried this command aa=fasta2AAStringSetlist("XXX.aa.fasta") for the AAString format but as I said there is an empty file for the result.

Do you have any suggestions to help me resolve this issue? Thank you for your time and this great tool.

Best regards.

Hi again, after a long time break I came back to great tool :)

My question is about DIAMOND blast file. Here is my file looks like:

When I tried the command

 c_binary <- classify_gene_pairs(
  annotation = pdata$annotation,
  blast_list = blast_data_list,
  scheme = "binary"
)

I got the fail like this even seq, annotation and diamond names are same:

Exited about final step to analysis :)

Thanks for your help and time,

Best

Hi, Fabricio
I have learned a lot about comparative genomics by studying your packages and articles,thanks.
Would you like to add the Phytozome API?

Best!