User: QVINTVS_FABIVS_MAXIMVS

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There's more than one way to hunt a CNV

Posts by QVINTVS_FABIVS_MAXIMVS

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BED to HDF5 in Python. Simple Script?
... I'm looking for some simple boilerplate script that efficiently converts a BED file (only Chrom Start End) to HDF5 in python. All the examples I see online are convoluted and bloated with functions that I do not need (HI-C/GTF). I do not need a CLI script, I would like to implement a BED -> H ...
python hdf5 bed written 13 days ago by QVINTVS_FABIVS_MAXIMVS2.3k
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Alternatives to CNVnator?
... I think I have put over 36 man hours in trying to get CNVnator to install. I have tried nearly every avenue, conda, environments, etc... and still cannot get it to install. I am at my wits end, what are comparable CNV calling algorithms for whole genomes that use read depth. Basically I'm looking ...
copy number variation cnv written 17 days ago by QVINTVS_FABIVS_MAXIMVS2.3k • updated 17 days ago by jared.andrews073.4k
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Samtools view -f "OR" operator possible?
... Quick question: Is it possible to do a `samtools view -f XXX` using a `OR` operator? Say if I wanted to get all reads that were unmapped (`4`) or supplementary alignments (`2048`). Is this possible? Because doing a `2052` is an "AND" (reads are unmapped and supplementary alignments which is imp ...
samtools written 3 months ago by QVINTVS_FABIVS_MAXIMVS2.3k • updated 3 months ago by dariober10k
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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 4 months 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 4 months ago by QVINTVS_FABIVS_MAXIMVS2.3k • updated 4 months ago by d-cameron2.1k
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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 7 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 7 months ago by QVINTVS_FABIVS_MAXIMVS2.3k • updated 6 months 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 7 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 7 months ago by QVINTVS_FABIVS_MAXIMVS2.3k • updated 7 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 9 months ago by QVINTVS_FABIVS_MAXIMVS2.3k

Latest awards to QVINTVS_FABIVS_MAXIMVS

Popular Question 7 days ago, created a question with more than 1,000 views. For Ggplot2: Plot X Axis As Y= 0 Line
Popular Question 3 months ago, created a question with more than 1,000 views. For Ggplot2: Plot X Axis As Y= 0 Line
Popular Question 3 months ago, created a question with more than 1,000 views. For Are XA: tagged reads == SA: tagged BWAMEM aligned reads?
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: Start position of structural variants in 1000 Genomes
Popular Question 7 months ago, created a question with more than 1,000 views. For Are XA: tagged reads == SA: tagged BWAMEM aligned reads?
Popular Question 7 months ago, created a question with more than 1,000 views. For Position of N nucleotides in reference genome
Popular Question 7 months ago, created a question with more than 1,000 views. For Ggplot2: Plot X Axis As Y= 0 Line
Popular Question 9 months ago, created a question with more than 1,000 views. For Combining ENCODE narrowPeak BED files across replicates
Popular Question 9 months ago, created a question with more than 1,000 views. For Ggplot2: Plot X Axis As Y= 0 Line
Popular Question 9 months ago, created a question with more than 1,000 views. For Ggplot2: Plot X Axis As Y= 0 Line
Good Answer 10 months ago, created an answer that was upvoted at least 5 times. For A: Start position of structural variants in 1000 Genomes
Great Question 16 months ago, created a question with more than 5,000 views. For Difference between Hard Clip and Soft Clip in Samtools CIGAR string
Great Question 16 months ago, created a question with more than 5,000 views. For cannot import pysam. Module has no attribute error
Prophet 16 months ago, created a post with more than 20 followers. For Difference between Hard Clip and Soft Clip in Samtools CIGAR string
Popular Question 16 months ago, created a question with more than 1,000 views. For Statistical Tests for Genetic Associations (Permutation)
Appreciated 16 months ago, created a post with more than 5 votes. For A: 1000Genome SV integrated map's power for SV filter
Popular Question 16 months ago, created a question with more than 1,000 views. For Are XA: tagged reads == SA: tagged BWAMEM aligned reads?
Popular Question 16 months ago, created a question with more than 1,000 views. For Combining ENCODE narrowPeak BED files across replicates
Popular Question 16 months ago, created a question with more than 1,000 views. For Ggplot2: Plot X Axis As Y= 0 Line
Popular Question 16 months ago, created a question with more than 1,000 views. For Position of N nucleotides in reference genome
Popular Question 16 months ago, created a question with more than 1,000 views. For Ggplot2: Plot X Axis As Y= 0 Line
Popular Question 17 months ago, created a question with more than 1,000 views. For Ggplot2: Plot X Axis As Y= 0 Line
Appreciated 17 months ago, created a post with more than 5 votes. For A: 1000Genome SV integrated map's power for SV filter
Popular Question 18 months ago, created a question with more than 1,000 views. For Ggplot2: Plot X Axis As Y= 0 Line

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