marbl/MashMap

About mashmap out

Opened this issue · 5 comments

jhtrujillo commented

Is there a manual to understand the output of the program?

cjain7 commented

Hi, as the README file says:

The output is space-delimited with each line consisting of query name, length, 0-based start, end, strand, target name, length, start, end and mapping nucleotide identity (estimate).

This is somewhat similar to the PAF output format used by minimap.

reachsagaya commented

Hi,
Iam using mashmap to compare recently assembled plant genomes. The genome Iam using has very high repeat content. Here is my code that Iam using:

mashmap -r ref.fa -q newassembly.fa --pi 100 -s 10000 -k 20 -f map -t 14
generateDotPlot png medium mashmap.out

Attached is my .png file. I see density of dots decreases as I move from chr1 to chr 9. How do I reduce the background noise and get a cleaner plot. Let me know if Iam missing something.

best regards
Sagaya
out

cjain7 commented

Hi, perhaps you can try using the one-to-one filter to avoid reporting paralogous matches. That would be -f one-to-one.

reachsagaya commented

Hi Chirag,

I did try both -f one-to-one and -f map. Both gives me almost similar results.

best regards
Sagaya

cjain7 commented

I see, did you also try increasing the minimum length cutoff, .. -s, that would get rid of smaller matches..