User: felipe-bita

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Posts by felipe-bita

<prev • 6 results • page 1 of 1 • next >
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Comment: A: Merging snp from different references into one vcf file
... HI, i'm very grateful for your help but i think it is not my problem. What i want to say is that despite the markers beeing found in different reference, they have the same information for all my samples. I want to find and remove this markers. ...
written 10 weeks ago by felipe-bita0
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Merging snp from different references into one vcf file
... HI guys, I'm here to ask your help in one thing that i have to do in my work, basically what i want to do is merge different VCFs files into one. This different VCFs are from different references used in the SNP calling, the specie that i study do not have a sequenced genome, so we are using genome ...
vcf snp gbs written 10 weeks ago by felipe-bita0
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Answer: A: Find clones in a population using a vcf file.
... Thank you, chrchang523. I used this method and i think it worked, i tested it with other populations, and mine had a lot of samples considered clones of the mother. The other populations that was no doubt about the apomictic chracteristic had only few samples >0.354. It helped me a lot. Thanks ...
written 5 months ago by felipe-bita0
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Find clones in a population using a vcf file.
... Hi guys. I am looking for an approach to find if there is clones in my population using a VCF file. Basically, i have a population of 130 individuals and the mother of them. This is a population for breeding that was made by a open cross. The 131 samples were genotyped using GBS and the variants cal ...
clones vcf population snp gbs written 5 months ago by felipe-bita0
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(Closed) Getting sequences from a fasta file.
... Hi guys, I am facing a problem, basically i have a fasta file, CDS of O. sativa, and i have a list of genes that i want to take from the CDS and write them in another fasta file, this list consists of 16k genes so i cant do it manually. I am using linux and i have a little experience in bioperl, if ...
fasta perl linux cds written 23 months ago by felipe-bita0
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Parameter to consider a hit as a gene copy
... Hi guys, i am trying to identify single copy genes in rice, what i've done so far was blast the CDS against itself and parsing the results with bioperl. My problem now is that i don't know what i use to consider a hit as a gene copy, i am calculating the proportions, alignmentlength/querylength and ...
gene alignment blast written 24 months ago by felipe-bita0 • updated 22 months ago by Biostar ♦♦ 20

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