User: Jeff.B.Gaither

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Posts by Jeff.B.Gaither

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Comment: C: Question about Somatic and Germline with homozygous and heterozygous
... I'm actually puzzled by this too (Sebastian, thanks for your response, but it doesn't totally answer my question.) In the above parapra, we get the conditions "Variants present in both samples are classified as somatic" "variant shared between samples are classified as germline" I think the OP was ...
written 5 months ago by Jeff.B.Gaither0
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Answer: A: Distribution underlying VCF QUAL - all sites or just those in VCF?
... Actually, perhaps a decent sample space would be, all the distinct calls made by the variant caller (in this case mpileup) by everyone in all of history. That is, 99% of the sites ever observed in history with QUAL=20 should be true mutations. A more formal definition would perhaps involve all possi ...
written 6 months ago by Jeff.B.Gaither0
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Distribution underlying VCF QUAL - all sites or just those in VCF?
... I'm wondering about the distribution which underlies a VCF QUAL score. Specifically, I understand that "A site with QUAL=20 has a 99% chance of being a true mutation," or more precisely (I think) "The collection of sites with QUAL=20 has the property that 99% of it consists of true mutations." ...
genome snp written 6 months ago by Jeff.B.Gaither0
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Comment: C: Running BWA on single-end data (i.e. only one fastq file) with "sampe" option
... Thanks for the suggestion. I checked ENA - there's only one file for this run. I know the distinction between "mate pair" and "pair end" is a common question - but they do definitely mention "mate pair." I'm not sure if this is amounts to a claim that their data should have two files, though. ...
written 14 months ago by Jeff.B.Gaither0
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Comment: C: Running BWA on single-end data (i.e. only one fastq file) with "sampe" option
... So, it's not paired-end - I tried a fastq-dump with the "--split-files" option, and just got the file SRR123_1.fastq. Devon Ryan, I'm really sorry, but I don't feel comfortable identifying the dataset (especially since there are others in the research group), though I can certainly sympathize with ...
written 14 months ago by Jeff.B.Gaither0
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Comment: C: Running BWA on single-end data (i.e. only one fastq file) with "sampe" option
... Thank you. I don't think this data IS paired-end - I'm only using the "sampe" option because they specifically mentioned in the paper that they used it. I've tried using "--split-3" option, and only got one fastq file. but I'll try with --split-files and see if I still get just one fastq file. ...
written 14 months ago by Jeff.B.Gaither0
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Comment: C: Running BWA on single-end data (i.e. only one fastq file) with "sampe" option
... Thank you. The thing is, I DON'T think this data is paired-end - I'm only using the "sampe" option because they specifically mentioned in the paper that they used it. I'm pretty sure I tried running fastq-dump using the "--split-3" option, and only got one fastq file. But I'll try with --split-file ...
written 14 months ago by Jeff.B.Gaither0
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Running BWA on single-end data (i.e. only one fastq file) with "sampe" option
... Hi all - I'm basically trying to replicate an alignment procedure from a paper. My data is in an SRR file at www.ncbi.nlm.nih.gov/sra. I've followed the pipeline (downloads and unzips human genome file GRRch38.fa.gz...) bwa index -a bwtsw GRch38.fa fastq-dump --split-3 SRR123 (at this point, I only ...
alignment written 14 months ago by Jeff.B.Gaither0 • updated 14 months ago by Pierre Lindenbaum98k

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