User: Wilber0x

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Wilber0x10
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Posts by Wilber0x

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Comment: C: finding specific SNPs in VCF files
... Thank you. SNPs from organism A are also in a vcf file. ...
written 7 days ago by Wilber0x10
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finding specific SNPs in VCF files
... I have a list of SNPs from one organism (organism A). I have genome skims of hybrids between organism A and other species. What methods can I use to see if SNPs from organism A are present in the hybrids? I have used bowtie2 to map genome skims to the same reference I used when finding SNPs for or ...
gene genome next-gen snp alignment written 7 days ago by Wilber0x10 • updated 7 days ago by Brice Sarver2.8k
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Decrease stringency of bowtie2
... I want to decrease the stringency of bowtie2 when mapping. How can I increase the overall alignment rate? My index is from one of two closely related organisms (species A). I want to find the sweet spot where my reads from species A align to the index at a very high rate, but reads from species B d ...
assembly next-gen sequence alignment written 12 days ago by Wilber0x10 • updated 12 days ago by h.mon27k
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Identifying unique SNPs between species
... I have 8 samples each with a VCF file made from aligning a genome skim of that sample to the same reference. I can see the number of SNPs for each sample in their individual VCF files, but I want to know how many SNPs and which SNPs are unique to each sample. Can I merge the VCF files into one to ...
vcf alignment snp written 8 weeks ago by Wilber0x10 • updated 8 weeks ago by finswimmer12k

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