User: QVINTVS_FABIVS_MAXIMVS

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Posts by QVINTVS_FABIVS_MAXIMVS

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Comment: C: BWA MEM Definition of a Primary Alignment
... Thanks for not answering my question. For chimeric reads (i.e for this example true split-reads that for SV informative) the difference between secondary and supplementary is semantic, a secondary alignment would map to another position but be clipped in a manner that is supporting a breakpoint. Som ...
written 13 days ago by QVINTVS_FABIVS_MAXIMVS2.3k
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BWA MEM Definition of a Primary Alignment
... Quick question: When bwa mem splits a read into a primary and a secondary/supplementary alignment, is the primary always the "left-most" on the query or is it the more confidently mapped alignment? Thanks. ...
wgs mem alignment bwa hts written 13 days ago by QVINTVS_FABIVS_MAXIMVS2.3k • updated 12 days ago by d-cameron2.0k
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Comment: C: How to make an Exon Junction BED file from ENSEMBL
... Thanks I think this will do it friendo ...
written 3 months ago by QVINTVS_FABIVS_MAXIMVS2.3k
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How to make an Exon Junction BED file from ENSEMBL
... I want to make an exon junction bed file to use for `olego` for the CAST strain of mouse. Ensembl has the reference genome and GTF files for this strain. Are there any tools to make an exon junction bed file for this strain? ...
exon junction written 3 months ago by QVINTVS_FABIVS_MAXIMVS2.3k • updated 9 weeks ago by Biostar ♦♦ 20
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Comment: C: Building A Splice Junction Library For Aligning Mrna Against The Rat Genome: Chr
... I want to make an exon junction bed file for CAST mouse strain. I can't get ALEXA-seq to work because of an unknown host error with cvs to ensembl. I imagine because it's quite old, do you happen to have a new version of the `alternativeExpressionDatabase/createExonJunctionDatabase.pl` program that' ...
written 3 months ago by QVINTVS_FABIVS_MAXIMVS2.3k
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Allele Age Software (Mutational Age)
... I'm looking for a software package to help estimate the allele age (mutational age) of neutral mutations in humans, given the allele frequency. Thanks :) ...
tools allele age mutational age written 3 months ago by QVINTVS_FABIVS_MAXIMVS2.3k • updated 3 months ago by pltbiotech_tkarthi170
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RNAseq Normalization for eQTL Mapping?
... How do you normalize RNAseq data for eQTL mapping? I have 200 samples with bulk RNAseq data, from that I generated matrix of TPM values for each gene. I also have a matrix of expected alignment counts and a matrix of read counts. I suppose I should use TPM for the eQTL mapping. If so, how do I n ...
qtl genetic mapping eqtl rna-seq written 5 months ago by QVINTVS_FABIVS_MAXIMVS2.3k
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10X scRNA-seq: Demultiplex into Samples with I1, R1, and R2 FASTQs
... I was given three files by a collaborator who is now on holiday and I'm looking for a quick answer for those who are not on holiday :) I have three FASTQs from a 10x v2 scRNA-seq run. The file with `I1` contains what I assume is the sample index (8mer) @E00527:118:HW5HWCCXY:7:1101:3315:1643 ...
10x single-cell demultiplex rna-seq written 5 months ago by QVINTVS_FABIVS_MAXIMVS2.3k • updated 5 months ago by swbarnes25.8k
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Comment: C: Documentation on VCI files? Or convert VCI to VCF?
... Thanks a ton, this is what I was looking for. ...
written 7 months ago by QVINTVS_FABIVS_MAXIMVS2.3k
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Comment: C: Documentation on VCI files? Or convert VCI to VCF?
... Diversity Outbred cohort of mouse lines that are derived from 8 founder strains. These mice are extremely genetically diverse, like a SNP every 600bp. I found this file from a FTP server for a lab at Jax ...
written 7 months ago by QVINTVS_FABIVS_MAXIMVS2.3k

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