Renaming chromosomes back to the orignal names?

[GLagunas-Robles]

Hello,

Thanks for this great program!

Is there an easy way to revert the chromosomes back to their original names for the plots produced by repeat observer? I think I see where I could change the names in the Setup_Run script, but I am not sure whether to change the variable there since there are a lot of hard-coded variables. Thanks!

[celphin]

Hi GLagunas-Robles,

Sorry for the very slow response - I have been away traveling. I'm just looking through these issues now.

The program initially ran with the chromosome/scaffold headers from the original fasta file but I found that too many errors were generated by the strange names in many fasta files.

Thus, I made the program rename the scaffolds/chromosomes starting with Chr1 for the first scaffold in the fasta, Chr2 for the second, and so on. At this stage, the program outputs a file (chromosome_renaming.txt) of the original scaffold names and the new names.

You could change the lines (95-106) that do this renaming of the scaffolds in the script (Setup_Run_Repeats.sh) to take your original file names instead of renumbering them. (See updated code below). However, if you do this you need to format for the names in your input fasta file as: Chr1, Chr2 etc. although I believe they could be in a different order e.g. Chr10 first then Chr1 etc. and the program should run fine.

I hope that helps. Let me know if you run into any problems or have any other questions.

Best wishes,
Cassandra

 # rename chromosomes
  touch ../chromosome_renaming.txt
  echo "Old_Name	New_Name" >> ../chromosome_renaming.txt
  count=1
  for filename in *; do
    new_name="${species}_${haplotype}_""$filename"
    # Rename the file
    mv "$filename" "$new_name"
    echo "$filename	$new_name" >> ../chromosome_renaming.txt
    ((count++))
  done
  echo "Files renamed"