need to map scaffolds to chromosomes: have mashmap outfile
0
0
Entering edit mode
22 months ago

Hi,

I have many genomes that are aligned to a reference genome composed entirely of scaffolds. I used mashmap to produce the mappings of these scaffolds to a fully sequenced, close relative that has chromosomes assigned (mashmap.out file). Now I need to use the mapping output from mashmap to actually find the locations of scaffolds on the chromosomes, so that I know which chromosome contains each scaffold. The goal is to be able to sliding window analyses for several summary statistics and to be able to analyze patterns across chromosomes. Can somebody please help me with this? Thank you!

mashmap scaffold chromosome • 439 views
ADD COMMENT

Login before adding your answer.

Traffic: 1302 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6