About mashmap out

[jhtrujillo]

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

[cjain7]

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]

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

[cjain7]

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

[reachsagaya]

Hi Chirag,

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

best regards
Sagaya

[cjain7]

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