About mashmap out about mashmap HOT 5 OPEN

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.

from mashmap.

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

from mashmap.

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

from mashmap.

Hi Chirag,

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

best regards
Sagaya

from mashmap.

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

from mashmap.