User: rrbutleriii

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rrbutleriii70
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Posts by rrbutleriii

<prev • 18 results • page 1 of 2 • next >
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Answer: A: VCF: Replacing RefSeq ID to chr in #CHROM
... Yeah, that was a real kick in the pants, as they didn't seem to post anything in the release notes, which still list them by chr1, chr2, etc. Best. documentation. EVAR. The easy solution is to have a renaming file for all the chromosomes of the format `old_name new_name\n` per [bcftools](http://w ...
written 4 days ago by rrbutleriii70
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Comment: C: Multiple rsIDs at chromosomal location?
... Follow up: So when parsing a vcf, would I then have to anticipate some variant callers giving me: `1 10051 rs1052373574;rs1326880612 A G,AC` I haven't ever seen that before, but I don't see anything to prohibit it. ...
written 9 months ago by rrbutleriii70
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Multiple rsIDs at chromosomal location?
... In the [VCF format][1], there is the option for the ID field to have multiple semi-colon separated values. In theory, there could be two dbSNP rsIDs in a single line (i.e. two indels at chr:pos), but for programming purposes, that should not happen, correct? dbSNP has merged all variants for a given ...
vcf annotation snp written 9 months ago by rrbutleriii70 • updated 9 months ago by Pierre Lindenbaum126k
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Applying lfcShrink to a time series analysis
... I am doing a time series analysis on a single cell line as in [Section 9][1] of the RNA-Seq workflow guide and was wondering if it is possible or advisable to apply lfc shrinkage to the result. library("fission") data("fission") ddsTC <- DESeqDataSet(fission, ~ strain + minute + stra ...
time-series deseq2 rna-seq written 10 months ago by rrbutleriii70
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Answer: A: From coverageBed to a list of reads per genes
... The reason the bam file is not working is because the bed file doesn't contain enough information to re-create reads. Perhaps there is a tool that attempts to reconstruct reads based on coverage beds, but that sounds...not good. You need a true bam/sam for featureCounts. I am unfamiliar with the ac ...
written 12 months ago by rrbutleriii70
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Answer: A: Questions about gene length and GC content in CQN normaliztion
... See this [post](https://www.biostars.org/p/317962/) for question one and two. Specifically, if all you need is gene length and GC, and you don't want to learn to access biomaRt directly, this will work (but takes a little time depending on the size of you matrix). library (EDASeq) ensembl_ ...
written 12 months ago by rrbutleriii70
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Comment: C: comparing RNA seq data from different studies using ratios
... The literal answer to 'would the ratio differ' is quite possibly. Thus my above that quantile normalized data shouldn't be compared in this way. Quantile normalization is not the same as the other normalization concepts of TPM/FPKM/RPKM. And even for those it is not recommended to compare across t ...
written 13 months ago by rrbutleriii70
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Pre-filtering transcriptome data by gene type
... I have seen in some transcriptome comparison analyses that the total RNA-seq data set is pre-filtered to only include protein-coding genes, or to exclude pseudogenes, or "short RNAs" ([Schwartzentruber et al](https://www.nature.com/articles/s41588-017-0005-8)). In a sense I understand this to imply ...
rna-seq non-coding rna transcriptome written 13 months ago by rrbutleriii70
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Answer: A: PacBio sequencing for variant calling?
... tl;dr The question to ask is the type of variation you are expecting to encounter; a non-systematic approach to be sure, but there is not a one size fits all solution. In my personal experience (TruSeq/Nextera Illumina several paired end types de novo and reference based, PacBio RSII p4c2/p5c3/p6c4 ...
written 13 months ago by rrbutleriii70
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Answer: A: comparing RNA seq data from different studies using ratios
... Read more in https://www.biostars.org/p/314454/ "The upper quartile FPKM (FPKM-UQ) is a modified FPKM calculation in which the total protein-coding read count is replaced by the 75th percentile read count value for the sample." https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/Expression_mR ...
written 13 months ago by rrbutleriii70

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