Question: Plotting Density Of Snps On Chromosomes
0
gravatar for sara.mehrabi
5 months ago by
sara.mehrabi40
Sweden
sara.mehrabi40 wrote:

Dear All,

I would like to make a graph in which I can compare SNPs of samples for each chromosome. I would like to know if there is an available tool for that/ if somebody has any experiences/ suggestions.

Thanks in advance. /Sara

snp chromosomes • 336 views
ADD COMMENTlink modified 5 months ago by Guy Reeves1.0k • written 5 months ago by sara.mehrabi40

Once you have a .VCF from tools like freebayes or pileup or other programs then you can use this tool 'VCF tools SlidingWindow'' to generate a list output which you can then graph in galaxy or outside. Unfortunately this tool is not available on usegalaxy.org. If you are using usegalaxy.org. then maybe somebody will suggest an method that will work there. Cheers

Guy

ADD REPLYlink written 5 months ago by Guy Reeves1.0k

Thanks Guy, i install this tool on our local galaxy and run it with VCF file I had. It worked and generate 6 files, but all of them are empty. do you have any suggestions? thanks, Sara

ADD REPLYlink written 5 months ago by sara.mehrabi40

I just ran a small .vcf on our instance. I have put the .vcf and the SNP density output on this drop box. Took< 20 seconds

https://www.dropbox.com/sh/sqj6okcrirq52bg/AACSOxfeMBxTy_sl5iiysEvNa?dl=0

Tell me if you get the same result. This will tell you if it is the tool or your .vcf

ADD REPLYlink written 5 months ago by Guy Reeves1.0k
1

thanks, I upload your vcf file in our galaxy server and run SlidingWindow, with Window size (in bp) 200000. it resulted an empty file. /Sara

ADD REPLYlink written 5 months ago by sara.mehrabi40

I think I used 2kb check output file in the Dropbox. If this is also empty, then it looks like the tool is not installed correctly . Ask your admin to check its dependencies.

ADD REPLYlink written 5 months ago by Guy Reeves1.0k
0
gravatar for Guy Reeves
5 months ago by
Guy Reeves1.0k
Germany
Guy Reeves1.0k wrote:

mistake

ADD COMMENTlink modified 5 months ago • written 5 months ago by Guy Reeves1.0k
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