User: zion22

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zion2240
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merilla
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15 hours ago
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6 months, 2 weeks ago
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Posts by zion22

<prev • 20 results • page 1 of 2 • next >
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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 2 days ago by zion2240 • updated 2 days ago by Philipp Bayer6.3k
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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 23 days ago by zion2240 • updated 22 days ago by Rob100
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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 8 weeks ago by zion2240 • updated 8 weeks ago by SMK1.8k
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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 8 weeks ago by zion2240
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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 3 months ago by zion2240 • updated 3 months ago by arup1.5k
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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 3 months ago by zion2240
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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 3 months ago by zion2240 • updated 3 months ago by arup1.5k
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Criteria for comparing genomes
... Hello I have a question for the more experienced, I am currently making a genomic comparison between my fungus and one of a paper (they are the same species), I would like to know what points I must take into consideration to determine whether my assembly, gene prediction, annotation and variant ca ...
genome assembly next-gen snp alignment written 3 months ago by zion2240
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join vcf file with annotations file?
... Sorry for the inconvenience, I'm very amateur in this field, I have a maybe stupid question. Is it possible to join the information from a vcf file to emapper.annotations file (produced by eggNOG)? ...
genome gene snp written 3 months ago by zion2240
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I can not run bcftools stats (help)
... Hi I would like to make statistics from vcf.gz files using bcftools stats, but when I try to run the following script, it generates files without weight my script is this: > bcftools stats -F "My_reference_genome.fasta" -s "My_vcf.gz_file.vcf.gz" > "/T1_.vcf.stats" Immediately ran the ...
genome written 4 months ago by zion2240

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Student 23 days ago, asked a question with at least 3 up-votes. For how to identify amino acids using snpEFF

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