svmu

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Hi there, when I used SVMU based on the nucmer, and get empty result besides cords.prefix.txt file. my command is ## alignment using nucmer nucmer -l 80 ara.fa nh.fa -p...

shehongbing

Segmentation fault

6

hi, I want use svmu to find structural variation between two genomes. here is my code: $MUMmer/nucmer --prefix NN2Wm82 Gmax_275_v2.0.fa NN1138-2.v0.5.fa $SVMU/svmu NN2Wm82.mm.delta Gmax_275_v2.0.fa NN1138-2.v0.5.fa NN_Wm82 but I met an...

shiyi-pan

the make problem

2

Hello, when I use make command, some errors appearred, like [-Wsign-compare] and [-Wunused-variable] as following: "g++ -g -Wall -std=c++0x -c svlib.cpp svlib.cpp: In function ‘void findInnie(std::vector&, mI&)’: svlib.cpp:39:34: warning: comparison...

ghost

Loss of chr information in cm.lastz.txt and sv.lastz.txt

3

Hello mahulchak, After I run svmu with a genome with two reference genomes, the out put of **cm.lastz.txt** and **sv.lastz.txt** shows no complete chromosomes for one reference genome . The...

clementmo

segmentation fault (core dumped) with the current version

1

I use the command "~/software/svmu/svmu test.delta 140001.fas 140028.fas h sam_lastz.txt test", it return "segmentation fault (core dumped) " and produce 3 empty files: cm.test.txt, cnv_all.test.txt and cords.test.txt. I have tried...

zhanghaoipp

lastz or Mummer

1

Hello mahulchak ! In the latest version , you use the alignment result of both mummer and lastz. But when the alignment result is different between these two softwares ....

liufy11

SVMU analysis using short read contigs.

1

Dear Mahul, I intend to use SVMU for calling variants between a reference and a newly sequenced strain of Drosophila. I have the contigs and also a scaffolded assembly for...

koushik1989

Can you tell me to define a Insert or Delete or a CNV according to the results of mummer?

liufy11