Restarting failed anchoring

[LZarri]

Hello,

My anchoring failed after the software detected non-reference genomes in the reference genome folder. How do I restart and keep using the xxx.delta and xxx.coords files?

Thanks, Liam

[nbedelman]

I have the same issue - mummer completed (after 8 days), and I'd like to continue from this point. Any suggestions about how to do this?

Thanks Nate

[LZarri]

I have found that, upon re-starting, it will overwrite the coords and delta file. What I decided to do was copy them to a different folder for later useage. If you are just looking to anchor reads, the coords file can be used to order the visualization of reads on Fst plots of Fst or Tajima's D. I am working on this now - happy to send code if it is helpful

[EBosi]

Hi, I will push an update to allow starting from mummer output, let me know how it goes when it's up

[nbedelman]

@LZarri that sounds really cool! Yes, I would totally be interested if you don't mind sharing. @EBosi thanks so much! Is this update available on conda?

[LZarri]

See below for R code to parse the coords file - the issue I had was that there are several regions of decreasing similarity where query read fits into the reference. But at least this is something to start with! For more info on the headers I used, see https://github.com/mummer4/mummer

bs <- read_delim("../genome/medusa_output/smb_50x_GCF_014851395.coords", skip = 5, delim= " ",col_names = c('S_Q', 'E_Q', NA, 'S_R', 'E_R', NA, 'LEN_1', 'LEN_2', NA, 'PERC_IDY', NA, 'LEN_Q', 'LEN_R', NA, 'COV_Q', 'COV_R', NA, 'TAGS')) %>% select(-c(X3, X6, X9, X11, X14, X17)) %>% mutate(PERC_IDY = round(as.numeric(PERC_IDY),0)) %>% filter(PERC_IDY > 80) %>% separate(TAGS, c('QUE_ID', 'REF_ID'), sep = '\t')

[nbedelman]

Very cool, thanks, I'll give it a try!

[EBosi]

Hi, I've pushed the commit by @gianlucacolotto in the main branch, let me know how it goes, I will close the issue for now.