Hi all,
I am using MiSeq paired end data which I recived from our sequencing facility, this data had already been cleaned using sythe and sickle. I have put the data through Fastqc to check the quality and revieved the following information:
File type Conventional base calls
Encoding Sanger / Illumina 1.9
Total Sequences 1270012
Filtered Sequences 0
Sequence length 20-251
I want to use Velvet as it seems to be the program used in most papers from within my field. I have installed Velvet from the ubuntu software center as I am not very skilled in using termial commands. It appeares to be the same version as from the velvet website (1.2.10).
The problem I have is that when I attempt to use velveth I get a segmentation fault.
I have reinstalled ubuntu as I read that I might have caused an issue when using a chmod command when following a "teach youself linux" book but this has not helped fix the issue.
I have also tried:
I have very little linux experiance and so I am not sure:
A) What this error means
B) How to fix it.
Any help would be greatly appreciated.
I am using MiSeq paired end data which I recived from our sequencing facility, this data had already been cleaned using sythe and sickle. I have put the data through Fastqc to check the quality and revieved the following information:
File type Conventional base calls
Encoding Sanger / Illumina 1.9
Total Sequences 1270012
Filtered Sequences 0
Sequence length 20-251
I want to use Velvet as it seems to be the program used in most papers from within my field. I have installed Velvet from the ubuntu software center as I am not very skilled in using termial commands. It appeares to be the same version as from the velvet website (1.2.10).
The problem I have is that when I attempt to use velveth I get a segmentation fault.
Code:
shell@shell-MS-1727:~$ velveth VPI_21 21 -shortPaired -fastq -separate VPI_R1.fastq VPI_R2.fastq Segmentation fault (core dumped)
I have also tried:
Code:
sudo apt-get install velvet Reading package lists... Done Building dependency tree Reading state information... Done velvet is already the newest version. 0 to upgrade, 0 to newly install, 0 to remove and 10 not to upgrade.
A) What this error means
B) How to fix it.
Any help would be greatly appreciated.
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