User: rightmirem

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rightmirem40
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Posts by rightmirem

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Comment: C: Recreating a Genomic reference (.fastq) from a BCF file
... Or maybe you mean I need a fastA, not a fastQ? ...
written 18 hours ago by rightmirem40
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Comment: C: Recreating a Genomic reference (.fastq) from a BCF file
... Thanks! I'm not sure what you mean when you say "fastq is not a reference-thing". I realize fastq is not "specifically" just for reference genomes. But I assume that it's the best file choice *for* a reference genome...in the sense that the original reference I used was a fastq run through HiSAT2 ...
written 18 hours ago by rightmirem40
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Recreating a Genomic reference (.fastq) from a BCF file
... I'm asking here before I go off half-cocked and try to build my own solution. Simply put, I have been using the **reference GRCh38**, created **BAM** files via ```HiSAT2```, and then **BCF** files using ```samtools mpileup | bcftools call | bcftools norm```. The BCF tools include the REF/REF mat ...
assembly next-gen snp alignment written 19 hours ago by rightmirem40
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Comment: C: Under what circumstances does "REF | REF" (or REF / REF) show up in the VCF/BCF
... "BCFTools could easily call 0/0 genotypes, but why would it?" Well, exactly my thought actually :D All my BCF files have "./.:." for samples that are REF/REF. But this one had "0|0" meaning it's not a variant, but a reference. So I couldn't figure out why they were there :D ...
written 6 days ago by rightmirem40
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Answer: A: Unusual reports from "bcftools stats" (making me question my data)
... Hi @kevin Wow and wow. Great response. And everything you say makes sense. "Welcome to bioinformatics" Ya :D (LOL) Thanks! (So, two more quick questions below) === **One thing for clarification** (I think my OP was unclear on this point)...due to filtering, my merged BCF file has NO ```0/0`` ...
written 6 days ago by rightmirem40
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Comment: C: Under what circumstances does "REF | REF" (or REF / REF) show up in the VCF/BCF
... Valid point. I wonder why my files have ```./.:.``` instead of "0/0" in the merged file? Maybe because ```bcftools```didnt know if the SNPs were 0/0 or just missing data? ...
written 7 days ago by rightmirem40
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Under what circumstances does "REF | REF" (or REF / REF) show up in the VCF/BCF file
... Potentially a very stupid question, but it wouldn't be my first ever :) So looking at the sample VCF files from this Biostars (```subset_hg19.vcf```), I see a bunch of lines with ```0|0``` in them. While I realize this means it has identified that position as matching ```REF | REF``` - why would ...
software error next-gen snp written 7 days ago by rightmirem40 • updated 7 days ago by WouterDeCoster23k
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Unusual reports from "bcftools stats" (making me question my data)
... I've generated a bunch (70) of VCF files containing SNP data for individual humans (diploid, one sample per file). I've also merged all 70 samples into a single BCF file. The issue is; when I ran ```bcftools stats``` I got some unusual (I think impossible) Allele Frequency data (based on what I se ...
software error next-gen alignment snp written 7 days ago by rightmirem40
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Faster (perhaps random) access to BAM files (for collecting statistics like average read depth)
... The title is not very clear. This is kind of two questions... Basically, I want to do things like discover the statistical information from a BAM (not SAM) file (so it's compressed. Part of the problem). 1. The immediate need is; I'd like to get an **average depth** for the entire file. 2. The l ...
bam sam snp written 12 days ago by rightmirem40 • updated 5 days ago by colindaven390
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Comment: C: How to validate the OVERALL quality of a VCF/BCF file (Data munging)
... Hi Kevin, I appreciate your thoughtful answer, and I'm in the process of obtaining some of that requested information. I'll touch base again when I have it. I just wanted to let you know I appreciated the comments. Best! Mike ...
written 12 days ago by rightmirem40

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