User: sara.mehrabi

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sara.mehrabi40
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New User
Location:
Sweden
Last seen:
2 months, 4 weeks ago
Joined:
6 months ago
Email:
s***********@slu.se

Posts by sara.mehrabi

<prev • 13 results • page 1 of 2 • next >
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ka/ks ratio- synonymous-nonsynonymous subsitution
... Hi All, I would like to calculate ka/ks ratio. I would like to know if some one has any experience? Best, Sara ...
ka/ks ratio synonymous nonsynonymus snp written 3 months ago by sara.mehrabi40 • updated 12 weeks ago by Jennifer Hillman Jackson23k
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EFF (Effect) filtering
... Hi All, I would like to filter my VCF file for Effect, exp: delete all the intergenic_region. I tried all the possibility I could think of and what ever they wrote as help, but nothing ! :( I wonder if some one has some solutions or similar experience? Thanks in advance. Best/Sara ...
filter snp effect written 4 months ago by sara.mehrabi40 • updated 4 months ago by Jennifer Hillman Jackson23k
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Comment: C: Plotting Density Of Snps On Chromosomes
... 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 ...
written 4 months ago by sara.mehrabi40
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Comment: C: SNPsift filtering problem
... First step: yes they are available. yes I did annotate with SnpEff. I am able to filter for DP, Quality, SRP, SAP one by one, but not all together. exp: I filter for DP, then filter for QUAL on the DP filtered file and so on and it worked. but still I am not able to filter for Effect. Thanks. ...
written 4 months ago by sara.mehrabi40
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Comment: C: Plotting Density Of Snps On Chromosomes
... 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 ...
written 4 months ago by sara.mehrabi40
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SNPsift filtering problem
... Dear All. I would like to filter my VCF file with SNPsift for DP, Quality, SRP, SAP and Effect (remove all the intergenic_region(MODIFIER||||||||||1). The first problem is that I can not filter for all of them together, I followed the instruction, but its not working. I can just filter for one of ...
filtering snpsift written 4 months ago by sara.mehrabi40
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Plotting Density Of Snps On Chromosomes
... 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 ...
chromosomes snp written 4 months ago by sara.mehrabi40 • updated 4 months ago by Guy Reeves1.0k
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Comment: C: snpsift filter fatal error
... Hi Jennifer, Thanks for your reply, Yes I remove the comments, because I thought my comment will make every thing more complicated. as you saw in my comment I got result once and with out changing any thing I got error afterward. because of some unknown reason for me, it start to work after I tri ...
written 5 months ago by sara.mehrabi40
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Comment: C: snpsift filter fatal error
... Hi Jennifer, here are the answers, I run the job on local, just because the tool (snpsift) was not available on Galaxy server as a result I can not send the bug from usegalaxy. the tool snpeff was working and used to produce the vcf file. we have the latest version of both galaxy and tool. as far ...
written 5 months ago by sara.mehrabi40
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snpsift filter fatal error
... Hi all, I want to use SnpSift Filter, but each time an error occurred. any idea? thanks in advance. /Sara Fatal error: Exit code 255 (Error) line 2:0 token recognition error at: '"' java.lang.RuntimeException: java.lang.RuntimeException: LexerNoViableAltException('"') at ca.mcgill.mcb.pcingola.s ...
snp written 5 months ago by sara.mehrabi40

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