Hi there.
Is there a manual for DNAdiff available somewhere?
I run the program with no issues, but at the end I cannot understand all the info I get back in all the results files:
Output files:
report: Summary of alignments, differences and SNPs
delta: Standard nucmer alignment output
1delta: 1-to-1 alignment from delta-filter -1
mdelta: M-to-M alignment from delta-filter -m
1coords: 1-to-1 coordinates from show-coords -THrcl .1delta
mcoords: M-to-M coordinates from show-coords -THrcl .mdelta
snps: SNPs from show-snps -rlTHC .1delta
rdiff: Classified ref breakpoints from show-diff -rH .mdelta
qdiff: Classified qry breakpoints from show-diff -qH .mdelta
Hi Jennifer, thank you for your help.
Unfortunately, for someone like me who uses the programs in Galaxy to avoid having to run them myself in Linux, the advice I find in the manual of mummer4 is a bit mute:
I don’t have access to the docs of the running program. I downloaded and unzipped the installation files for mummer-4.0.0rc1, but there is no docs folder or anything like that. I guess a very good service by Galaxy would be to make these docs available through the DNAdiff page. I would be very grateful…
Also: the 2 links at the bottom of the DNAdiff page don’t work: both open up empty pages.
Unfortunately, the Tutorials of the mummer4 page don’t mention DNAdiff.
Thank you a lot. Regards.
Thank you Jennaj.
Since we’re at it, I would like to point out another small flaw: in the result files of DNAdiff, when I view them within the Galaxy web page, I can see headers for each column (ex. Seq ID Feature Type Feature Start Feature End Feature Length Column 6 Column 7), but these headers are not present in the downloaded .tabular (or .tab) files. The headers would obviously be quite helpful to have in the files…
Thanks again. Regards.
I saw that too, and am guessing that was on purpose (to make it easier to parse the files with other tools, in a workflow or similar).
You could open another ticket at that same place – maybe ask that the tool form includes an option to print out the headers into the outputs? Having a toggle would allow for both ways to use the outputs.
Let me know what you decide, and I can do that later today instead!
Sorry that I wasn’t clearer: I meant that you could also open up an issue ticket at the Github repository where I had opened the other issue. Do you want to try doing that now (instead of posting the request here again), or do you want me to create it? No problem either way.
