the result

[wenjiexiaomeng]

scaffold100000|size4398 C27495846419.0 4398 287 1003 1288 287 1 1 1 0-2400 scaffold100000|size4398 C27567557919.0 4398 322 1800 2026 322 95 2 2 0-1000 scaffold100000|size4398 scaffold13097019.4 4398 3412 2129 2283 167 10 4 4 0-112-1-250 scaffold100000|size4398 scaffold44576520.6 4398 5548 1458 1695 3065 2826 3 3 0-202-3203867 4222 1115 757 7 7 0-14124-71-2332-58-60 scaffold100001|size4398 C2721590907.0 4398 209 4144 4248 140 36 0 0 00 scaffold100001|size4398 scaffold133571412.7 4398 1391 3481 4011 809 1347 28 28 0-216-1-1-1-1-1-1-1166-80 scaffold100001|size4398 scaffold4287048.3 4398 1847 525 792 269 4 7 7 025-1054511-460 scaffold100001|size4398 scaffold86268516.5 4398 1028 1381 1726 281 627 8 8 0-24-1720 scaffold100002|size4398 C27479571713.0 4398 281 584 858 281 7 0 0 00 scaffold100003|size4398 C27185330824.0 4398 203 931 1133 1 203 1 1 00 ##############################################333

This is the result in my merged.fasta, what does this mean? I thought may be there are some problems here....

[mahulchak]

Could you please describe the commands and steps you used ?

On Sun, Dec 17, 2017, 17:18 wenjiexiaomeng notifications@github.com wrote:

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[wenjiexiaomeng]

Hi, These are my commands: ############################################################################# /def/software/quickmerge-master/MUMmer3.23/nucmer --mum -c 100 -D 5 -d 0.12 --extend -g 90 -l 100 -p qingxia_nucmer qingxia_bwa.final.scaffolds.fasta qingxia.scafSeq /def/software/quickmerge-master/MUMmer3.23/delta-filter -i 50 -l 100 -m -q -u 50 qingxia_nucmer.delta>out_qingxia.delta.out /def/software/quickmerge-master/quickmerge -d qingxia_bwa.final.scaffolds.fasta -q out_qingxia.delta.out -r qingxia.scafSeq -hco 0.5 -c 1.5 -l 20000 -ml 20000 ############################################################################ I ran this step by step, and there were no errors . I noticed that there are some spaces in my scaffold name so I rename them and running it again.Would this be the reason? Thanks for your help.

Best, Wenjie

[mahulchak]

Hi Wenjie, I would recommend you to follow the nucmer and quickmerge commands as described in the GitHub manual first and then you can tweak them as you wish. following your files names, I am guessing qingxia_bwa.final.scaffolds.fasta and qingxia.scafSeq are the two assemblies? I am a little confused by the file name "qingxia.scafSeq". Are you sure that it is a fasta file ? Please run nucmer and delta-filter with the parameters as mentioned in the manual.

To run quickmerge, please follow the order of the commands as mentioned in the manual. E.g. quickmerge -d out_qingxia.delta.out -q qingxia.scafSeq -r qingxia_bwa.final.scaffolds.fasta -hco 5.0 -c 1.5 -l 20000 -ml 20000

[wenjiexiaomeng]

Hi,

I finished it by your suggestions, and I will try with different parameters. Thanks a lot! (I confounded the two parameters -d and -q...)

Best, Wenjie

[mahulchak]

Cool

On Wed, Dec 20, 2017, 21:37 wenjiexiaomeng notifications@github.com wrote:

Hi,

I finished it by your suggestions, and I will try with different parameters. Thanks a lot! (I confounded the two parameters -d and -q...)

Best, Wenjie

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