User: steven.lin.pur

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Taiwan
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1 year, 6 months ago
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Posts by steven.lin.pur

<prev • 6 results • page 1 of 1 • next >
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Comment: C: calling variants between two strains
... Thank you for the advice. I have some problems when practicing it however, can you please help me? When I merge and compare the two VCF files, I can't tell if there is a difference between the two strains when the following case occur: Reference has a genotype A at locus 100; Strain i has a genot ...
written 21 months ago by steven.lin.pur10
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Comment: C: BWA mem how to know if a read is mapped uniquely?
... Sorry, it turns out that BWA does still give XA tag..... I was reading the latest SAM file spec and I can't find the XA tag anymore. I thought this means that the XA tag isn't available anymore. I'm a bit confused about the output though. If there is an XA tag, doesn't mean that it is a non-unique ...
written 23 months ago by steven.lin.pur10
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Comment: C: BWA mem how to know if a read is mapped uniquely?
... Thank you, I'll try that. I'm just wondering why hasn't there been a tool to perform such a task. This seems to be a common task when handling bam/sam files.  ...
written 23 months ago by steven.lin.pur10
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BWA mem how to know if a read is mapped uniquely?
... I have read many posts regarding this question. The XT, XA tag doesn't seem to be used anymore by BWA mem, so I can't use them to identify uniquely mapped reads. Some posts said that multiple hits are to be assigned a quality score of 0. However, I don't have any links to confirm if this is still t ...
alignment bwa written 23 months ago by steven.lin.pur10 • updated 23 months ago by Lemire/OICR350
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Comment: C: calling variants between two strains
... Thank you for the great advice! it is my understanding that Mummer needs a reference too to perform alignment. are you suggesting that I map one of the strain to the reference, creating a aligned genome of one strain, then used that aligned genome as a reference to map the other strain? Thanks aga ...
written 23 months ago by steven.lin.pur10
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calling variants between two strains
... (newbie alert) I'm trying to find the sites of variants between two strains. I've map them both to the same reference. However, I don't know what the next step should be. I've used freebayes to call the SNP between the strains and the reference, but I don't know how to find the variants between the ...
samtools freebayes vcftools snp written 23 months ago by steven.lin.pur10 • updated 23 months ago by apelin20460

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