how to get the file of N2 SNP filtered

Question: how to get the file of N2 SNP filtered

8 months ago by

17317822349 • 10 wrote:

Dear sir/madam: How do you do ? i want to find the mutant gene under the background of CB4856 SNP ,so i need both HA reference gennome file and the file of N2 SNP filtered and unfiltered ,right ? but ,i have trouble in geting them. in fact ,the experiment was executed in this way: P0 wildtype (CB4856) X mutation(N2)

F1 Heterozygote | F2 Homozygous(Whole genome sequencing) I will appreciate it If you can give me some suggestions. Thanks a lot.

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modified 8 months ago • written 8 months ago by 17317822349 • 10

8 months ago by

Wolfgang Maier • 600

Germany

Wolfgang Maier • 600 wrote:

It is, at least, somewhat unusual to try to start with a Hawaiian reference. Normally, you'd use an N2 reference and a list of Hawaiian SNPs instead. From a previous thread it sounded as if you had access to both of these. Correct?

Maybe you should follow this tutorial first. The MiModD tools used there are now available at usegalaxy.org and, compared to the old CloudMap suite of tools, make for far simpler workflows. Just one note about the tutorial: when working on usegalaxy.org you should use bowtie2 instead of MiModD's native Read Alignment tool at the alignment step and the SnpEff Variant effect and annotation tool instead of the MiModD Variant Annotation tool. The details are explained here.

ADD COMMENT • link written 8 months ago by Wolfgang Maier • 600

8 months ago by

17317822349 • 10

17317822349 • 10 wrote:

Thanks so much for your answer .Actually ,i had ever used an N2 reference and a list of Hawaiian SNPs ,and the question is that the maximum value of Y- axis is 0.7 ,less than 1,so that the curve graphs can not get its peak value ,and i cannot find the mutant region. As a result ,i need an Hawaiian reference and a list of N2 SNPs instead.And in fact ,i do not know where and how to download them.

ADD COMMENT • link written 8 months ago by 17317822349 • 10

the maximum value of Y- axis is 0.7 ,less than 1,so that the curve graphs can not get its peak value ,and i cannot find the mutant region

I don't think I understand this completely. Are you saying you are getting a peak (it would be nice if you could tell us with which tool, by the way) at 0.7, but you are not trusting it because it is < 1, or is it that the graph is clipped at 0.7 so you cannot determine where the peak is?

Whatever the problem is though, why do you think that exchanging the reference and the SNPs list will help you? You could certainly get the Hawaiian reference from the Wormbase ftp site, but I'm not sure where you would get an N2 SNPs VCF file from. Are you still using CloudMap and hoping that the Variant Discovery Mapping tool will give you better results than the Hawaiian Variant Mapping tool? Really, it is hard to provide useful help without knowing the details.

ADD REPLY • link written 8 months ago by Wolfgang Maier • 600

Duplicated Q&A - redirected back here: https://biostar.usegalaxy.org/p/27373/

ADD REPLY • link written 7 months ago by Jennifer Hillman Jackson ♦ 25k

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