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7.0 years ago
misbahabas
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70
hello
Is it possible to annotate single gene by snpeff ?
anyone have idea about it
hello
Is it possible to annotate single gene by snpeff ?
anyone have idea about it
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Like previous threads: EXPLAIN MORE. Give information about what you are doing (MSA of multiple species converted to vcf).
Put some d*mn effort in your questions and don't make this too hard for people trying to help you.
snpeff annotate variant , what do you mean by annotate gene ?
I want to annotate variants from genes sequences. I do MSA of one gene in multiple species and convrt into vcf and now want annotate variants from this vcf . I can annotate variants from chr or whole genome but with gene sequence I do not understand how to do it , because snpeff annotate variants chromosome wise
What exactly are you trying to do? Generally SNP discovery is done for a single species.
I am trying to annotate vcf which contain position of genes instead of genome. after multiple sequence alignment I used snp-sites to convert fast into vcf which contain snp position in genes Like
Now i should annotate these variants using snpeff and variant effect predictor , to find misssense variants, but I cannot understand how to do it because its a gene sequence and vcf file contain gene position not genome position
Is it possible to annotate vcf which contain gene positions in different species by snpeff?
I don t think you can you need genomic position , and i m not sure MSA work
there is any other tool which take gene positions(not genomic positions) as a input in vcf format, to do annotation of gene variants ??
I never heard about this kind of tool. In your example where is the gene name/ID information for example ? How the tool can guess the gene name to translate the mutation consequences ?
By the way I m not sure you are using the good "pipeline"/algorithm to find a solution to your question.
i also try this
but Its not usefull, results remain same, tool considered chromosomes position not gene positon
output like this
This output same as when gene id/name not used. its not effect the output How can i confirm its true or false
is there any way to convert gene positions into genomic positions ?
First of all i think you should read what you are writing because you can t explain you problem in 1 line !
What is MSA ? (you too lazy to write it completely and i m an ignorant )
If i understood a peace of what you saying you tried to annotate a vcf which got gene position instead of genomic position ?
MSA = Multiple Sequence Alignment.
MSA = Multiple Sequence Alignment.
yes i want to annotate a vcf which got gene position instead of genomic position ?