[MUMmer-help] help with PROmer

[NOUR M. M. <nmm...@sc...>]

Hello!

I'm using MUMmer for the first time, and I'm running it on Ubuntu WSL, in case this information is relevant.

I'm following the steps listed on your examples tutorial website<http://mummer.sourceforge.net/examples/#promer> using the following files: ecoli.fna and baumannii.fna

I'm currently stuck at this step:
2.4.3. Running show-aligns

To view all the pairwise alignments between two of the input sequences, we need to run the promer.delta file through the show-coords utility.

show-aligns promer.delta "D_melanogaster_2Rslice" "3214968" > promer.aligns

This command will print all of the pairwise alignments stored in the promer.delta file for the sequences "D_melanogaster_2Rslice" and "3214968". Output is to stdout, so we have redirected it into the file, promer.aligns. If the alignments do not fit within your screen width, or you would like them to be printed on longer lines, the screen width can be adjusted with the -w option. Since show-aligns only displays the alignments between two sequences, it will have to be run separately for each desired pair of sequences.

>From what I've understood, the names between the double quotation marks are supposed to be the ref ID and the qry ID, but I have no idea where the number "3214968" came from in the command line on your website. and I have no idea what it's supposed to represent. In earlier steps, the file names used were
D_melanogaster_2Rslice.fasta D_pseudoobscura_contigs.fasta
so I can see where the D_melanogaster_2Rslice came from.

I tried running the following codes, alongside all permutations of the sequence lengths and the names of the file:

show-aligns promer.delta "ecoli" "baumanmnii" > promer.aligns
show-aligns promer.delta "baumanmnii" "ecoli" > promer.aligns
show-aligns promer.delta "baumanmnii" "9283306" > promer.aligns
etc., etc.,


What confuses me even more, is that the step before it <http://mummer.sourceforge.net/examples/#:~:text=2.4.2.%20Running%20show%2Dcoords>  (2.4.2) doesn't show the coordinates unless I delete the
">  promer.coords" part and even when I do, the 2.4.3 step doesn't work.
I would appreciate any input on what I'm meant to do now as I am very confused. If there are any other resources you could direct me to I would also be much obliged.

Thank you in advance.

Regards,
Nour Mustafa