User: sami

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sami20
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2 days, 18 hours ago
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1 week, 5 days ago
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Posts by sami

<prev • 39 results • page 1 of 4 • next >
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Comment: C: k-mer finding and counting
... i have not google it , i ll try ...
written 2 days ago by sami20
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Comment: C: FreeBayes :the tag "DP4" is not defined in the VCF header
... yes, you can get it using the new version of bcftools , ...
written 2 days ago by sami20
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k-mer finding and counting
... I have a fastq file. I want to have k-mers and their abundance numbers. can you give me some tools to do this! thank you ...
k-mer written 2 days ago by sami20 • updated 2 days ago by wljlinksly20
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Comment: C: Why Does Mpileup Skip some variants ?
... you can close it. thank you ...
written 2 days ago by sami20
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Comment: C: FreeBayes :the tag "DP4" is not defined in the VCF header
... DP4 gives depth of coverage in reverse and foward strain. if there is mutation in fowards but not in reverse , we can't take it. normally , if mutation exist in foward , it must be present also in reverse. We use Depth because we can't filter variant using mapp quality . MAPQ is not a good filter. h ...
written 2 days ago by sami20
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Comment: C: FreeBayes :the tag "DP4" is not defined in the VCF header
... ...
written 3 days ago by sami20
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Comment: C: Why Does Mpileup Skip some variants ?
... Yes i know already that there a mutation ...
written 3 days ago by sami20
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FreeBayes :the tag "DP4" is not defined in the VCF header
... Using FreeBayes i get vcf file without DP4 field! How can i force DP4 to be present in my vcf. ...
freebayes written 3 days ago by sami20
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Comment: C: Why Does Mpileup Skip some variants ?
... Because i don't have more detail . FreeBayes is good but it dosen't give me DP4 in vcf. I have the same problem without ploidy 1 with bcftools! Do you have any idea how can i force DP4 to be present in vcf ? what parameters should i give to FreeBayes ! When i check DP4 , i get this error : Er ...
written 3 days ago by sami20
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Comment: C: Why Does Mpileup Skip some variants ?
... My problem is: In this position : ====> T (Ref: with depth=94) ---> C (Variant: with depth=94) T and C have the same depth of coverage , so bcftools don't call this variant. I need to tell bcftool to call variant when there is the same depth of coverage in the reference and in the mutant ...
written 4 days ago by sami20

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