Find the accurate relationship between initial contig and final scaffold

[LIZW2019]

Hi, Thank you for your amazing software! Now I have successfully get the chromosomal level assembly after running run-asm-pipeline-post-review.sh, but I need to know the updated location of the contigs relative to chromosomes to update my annotation(I do it in the contig level), I found the ouput files other than hic.(like assembly) might can help me, but I am not sure the meaning of each column. Do you know which output can help me, and can you briefly explain the meaning of the format? Thank a lot! All my ouput is like this:

Best wishes, LIZW

[dudcha]

Hi LIZW,

Thanks for the kind words. Here is a slide re assembly format that might be of help. In this case _HiC.assembly (DNA Zoo convention) is the same as .FINAL.assembly in your output:

https://docs.google.com/viewer?a=v&pid=forums&srcid=MTQwMjA4ODQ1NDM4NDQ3NjQ4NzABMDg0NTM3ODMxMzA3NTM1MTg3MzcBY25kcHRhUkVBd0FKATAuMQEBdjI&authuser=0

(Maybe you will find also some comments on this thread useful: https://docs.google.com/viewer?a=v&pid=forums&srcid=MTQwMjA4ODQ1NDM4NDQ3NjQ4NzABMDg0NTM3ODMxMzA3NTM1MTg3MzcBY25kcHRhUkVBd0FKATAuMQEBdjI&authuser=0 )

Best, Olga

[LIZW2019]

Dear Olga,

Thanks for your warm reply! I found the files "canu_pilon.final_asm.scaffold_track.txt" and "canu_pilon.final_asm.superscaf_track.txt" more useful for me, it shows the change before and after. I would like to know the meaning of "+" "-" in the scaffold file: Thank you so much!!

Best, LIZW

[dudcha]

LIZW,

This is calculated based on the assembly file. Please note that this corresponds to rawchrom stage and does not include final gaps between draft sequences. Sign refers to whether the whether the draft needs to be reverse complemented or not.

Best, Olga

On Dec 13, 2019, at 1:01 AM, LIZW2019 [email protected] wrote:

 Dear Olga,

Thanks for your warm reply! I found the files "canu_pilon.final_asm.scaffold_track.txt" and "canu_pilon.final_asm.superscaf_track.txt" more useful for me, it shows the change before and after. I would like to know the meaning of "+" "-" in the scaffold file:

Thank you so much!!

Best, LIZW

— You are receiving this because you commented. Reply to this email directly, view it on GitHub, or unsubscribe.