User: tbb21

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tbb2110
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2 months ago
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8 months, 2 weeks ago
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t****@duke.edu

Posts by tbb21

<prev • 11 results • page 1 of 2 • next >
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Comment: C: Lots of alleles in the same place?
... In addition, some of the DP4 entries look like: `0,0,8,0` does this mean that at this position *none* of the non mutant alignments were of a high enough quality to pass the filter and only variants were? ...
written 9 weeks ago by tbb2110
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Lots of alleles in the same place?
... I have short (20 bp) sequencing reads for DNA that has been in e. coli undergoing different rates of SOS response (inducing mutations in the DNA). When I use bcftools to do variant calling of these reads, mapping them back to the ~10,000 original 20 bp long DNA sequences, I seem to get variants at p ...
alleles snps bcftools variants written 9 weeks ago by tbb2110 • updated 9 weeks ago by Kevin Blighe45k
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I16 Info Tag
... Hi all, bioinformatics noob here. I have been trying to call variants and don't fully understand what the I16 tag's first 4 entries mean. I found this table: 1 #reference Q13 bases on the forward strand 2 #reference Q13 bases on the reverse strand 3 #non-ref Q13 bases on the forward stra ...
bcftools snp mpileup sequencing written 7 months ago by tbb2110 • updated 7 months ago by finswimmer11k
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Comment: C: Changing samtools mpileup I16 calculations?
... This is a great question I would also love the answer to. ...
written 7 months ago by tbb2110
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Comment: C: VCF/BCF File format QS score in INFO header
... I have the exact same question. Can't find an answer anywhere and have no idea why this hasn't been answered! ...
written 7 months ago by tbb2110
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Comment: C: Filtering Read Quality - Cant remove all reads that have a single base below a t
... Thanks re the gold standard and I have now saved and uploaded all of the relevant plots! ...
written 7 months ago by tbb2110
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Comment: C: Filtering Read Quality - Cant remove all reads that have a single base below a t
... Sorry its a single base. I have corrected this. ...
written 7 months ago by tbb2110
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Comment: C: What does <*> mean in a vcf file?
... Upon a second reading I think it may be a wildcard placeholder for any other alternative allele? So if I have an output like this: A (REF) G,<*> (ALT) and the PL is: 0,57,255,78,255,255. So does this mean that the PLs correspond to: AA, AG, GG, A<*>, G<*>, <*><*>? ...
written 7 months ago by tbb2110
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Filtering Read Quality - Cant remove all reads that have a single base below a threshold
... Hi Biostars, I am new to handling sequencing data so this is my first time posting here! So I am trying to remove all reads with any of their base pairs below a threshold quality score, here 32. I have tried using the FASTQ quality_filter using `fastq_quality_filter -q 32 -p 100 -o output.fastq.g ...
filter fastx quality-score sequencing written 7 months ago by tbb2110 • updated 5 months ago by Biostar ♦♦ 20
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Comment: C: Fastq Quality Filter Parameters
... Can you give any comments on what the gold standard is. For example, all reads needing to be above a Phred score of 32? ...
written 7 months ago by tbb2110

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