User: zion22

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zion2260
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60
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New User
Location:
merilla
Last seen:
4 months ago
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1 year, 11 months ago
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Posts by zion22

<prev • 33 results • page 2 of 4 • next >
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Mapping an unique KEGG pathway
... Hi, sorry for my ignorance. I would like to know how I could check if all the genes of an unique KEGG PATHWAY (e.g. GO:0009718) are present in my genome? and if possible, is there a tool that performs automatic pathway mapping? Thanks ...
genome gene next-gen written 6 months ago by zion2260 • updated 6 months ago by N15120
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Sugestion for circular visualization of genome
... good day, I know this topic must be very common around here, but I would like you to recommend me a good genome visualizer for dummies (easy to use and looks nice), sorry but I am very new in this area thanks ...
genome gene written 7 months ago by zion2260 • updated 7 months ago by Alex Reynolds31k
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optimize post Spades assemblies
... Hi I have a question for you, how can I optimize my assemblages of a de novo genome (without any kind of similar genome), since I currently use Spades for this process, but I have noticed that the amount of contings that I generate are many, and I would like to decrease the amount as much as possibl ...
genome assembly next-gen written 15 months ago by zion2260 • updated 15 months ago by JC12k
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Augustus output (GFF file) to Anvi`o
... Hi, thanks for reading this. I'm very amateur in this area and I have a question, I am using Augustus to predict genes of a eukaryotic organism and I would like to integrate the output of Agustus (gff file) to the contigs file of Anvi´o. I tried to use GFFPraser but couldn't. So if anyone could ...
genome gene sof written 16 months ago by zion2260 • updated 16 months ago by Philipp Bayer6.8k
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how to identify amino acids using snpEFF
... hi, thanks for reading this, I have a doubt, I am identifying snp using **snpEFF** with the following command: snpEff eff -c snpEff.config my_genome -s output_.html -v "variants/imput_.vcf.gz" > "variants/output_.vcf.gz" but I would also like to obtain the amino acid changes that were made ...
gene genome next-gen snp written 17 months ago by zion2260 • updated 17 months ago by Rob120
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filter non synonymous using SnpSift
... Hi. Thank for reading this I have a problem, when i used the next command from SnpSift software: java -jar SnpSift.jar filter "( EFF[0].EFFECT = 'NON_SYNONYMOUS_CODING' )" -f my_original_file.vcf > NON_SYNONYMOUS_file.vcf -v The program didn't filter it as I wish. because when I compare ...
software error sequence snp written 18 months ago by zion2260 • updated 18 months ago by AK1.9k
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Comment: C: extract polyformisms non synonymous using SnpSift
... Hi. Thank you so much for helping me. but I have a problem, when I run the next command: java -jar SnpSift.jar filter "( EFF[0].EFFECT = 'NON_SYNONYMOUS_CODING' )" my_original_file.vcf > NON_SYNONYMOUS_file.vcf when I compare the two files, original and filtered, are exactly the same, eve ...
written 18 months ago by zion2260
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extract polyformisms non synonymous using SnpSift
... Hi, sorry to bother you. I ask in this forum why maybe someone can help me, some of you know how I could extract polyformisms non synonymous using SnpSift? and if you have an example of the command I appreciated it very much. Thank you ...
genome next-gen sequence snp written 19 months ago by zion2260 • updated 19 months ago by Arup Ghosh2.7k
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Comment: C: Advanced use of snpEff
... Hi I used this command snpEff -c snpEff.config GRCh37.75 variants_.vcf.gz" > variants_.snpEff.vcf I know that this way i get three output files, the annotated vcf file, a text file summarizing the number of variant types per geneand and HTML file containing summary statistics, but i just w ...
written 20 months ago by zion2260
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Advanced use of snpEff
... Hello I have two questions for this wonderful forum: 1- I have results of snpEff (vcf files) but some of you know the command to generate the statistics from this file, normally snpEff does it when I run it, but I just want the statistics without running the whole program. 2- How can I filter th ...
snp written 20 months ago by zion2260 • updated 20 months ago by Arup Ghosh2.7k

Latest awards to zion22

Student 17 months ago, asked a question with at least 3 up-votes. For how to identify amino acids using snpEFF

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