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Question: Need help with "Map with BWA for Illumina" tool
0
gravatar for zhigang.zhu
4.2 years ago by
zhigang.zhu • 0
Denmark
zhigang.zhu • 0 wrote:

 I don't know why the mapping procedure doesn't work.  My g-DNA sequence is fatsaq format, it can't show in the down list. so I changed the fastaq formate into fastaqillumina, and then i can find it in the ist. when I map these short sequence to the reference genome, the mapping function doesnt work. how to solve this problem? 

 

Thanks a lot.

 

Tool name: Map with BWA for Illumina
Tool version: 1.2.3
Tool ID: toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3
ToolShed URL: https://toolshed.g2.bx.psu.edu/view/devteam/bwa_wrappers

 
map-with-bwa-for-illumina • 1.1k views
ADD COMMENT • link •
modified 4.2 years ago by Bjoern Gruening ♦ 5.1k • written 4.2 years ago by zhigang.zhu • 0
0
gravatar for Bjoern Gruening
4.2 years ago by
Bjoern Gruening ♦ 5.1k
Germany
Bjoern Gruening ♦ 5.1k wrote:

Hi,

your format is most probably in the fastqsanger format. If your format is really in fastqillumina format your need to convert it with 'FASTQ Groomer' beforehand. For more information please have a look at the different fastq formats: http://en.wikipedia.org/wiki/FASTQ_format
ADD COMMENT • link written 4.2 years ago by Bjoern Gruening ♦ 5.1k

Thanks for your response. It still doesn't work. I used 'FASTQ Groomer' to convert my sequence. When mapping these sequence, nothing happened. I can not find out the problem.

ADD REPLY • link written 4.2 years ago by zhigang.zhu • 0

What means, "does not work" or "nothing happend"? Do you get an error message? Maybe you do not to groom the file. Just change the filetype to fastqsanger.

ADD REPLY • link written 4.2 years ago by Bjoern Gruening ♦ 5.1k
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