User: QVINTVS_FABIVS_MAXIMVS

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Posts by QVINTVS_FABIVS_MAXIMVS

<prev • 225 results • page 1 of 23 • next >
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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 4 weeks ago by QVINTVS_FABIVS_MAXIMVS2.2k
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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 7 weeks ago by QVINTVS_FABIVS_MAXIMVS2.2k • updated 7 weeks ago by swbarnes24.8k
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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 12 weeks ago by QVINTVS_FABIVS_MAXIMVS2.2k
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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 12 weeks ago by QVINTVS_FABIVS_MAXIMVS2.2k
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Documentation on VCI files? Or convert VCI to VCF?
... I never came across a VCI file and I'm having some trouble finding documentation on the format. Is anyone familiar with these files? Is`ANCHOR` the reference allele, why is it absent for some variants? This is from one of the founders for the DO mouse lines. ##CREATION_TIME=05/23/2016 18:21: ...
vcf vci written 12 weeks ago by QVINTVS_FABIVS_MAXIMVS2.2k
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Comment: C: Concat VCFs with some shared samples
... Because the merge tools do not like the duplicate sample names. And if you `--force-samples` then you get a second column of the sample name `NA12878` becomes `2:NA12878` and that's more of a headache . I'm looking for a quick fix out of laziness. This can be done with a quick script, but I have sp ...
written 3 months ago by QVINTVS_FABIVS_MAXIMVS2.2k
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Comment: C: 1000Genome SV integrated map's power for SV filter
... The link to AnnotSV seems to be broken. If you are an author on the paper, do you mind fixing the link please? www.lbgi.fr/AnnotSV/ ...
written 3 months ago by QVINTVS_FABIVS_MAXIMVS2.2k
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Concat VCFs with some shared samples
... Say I have 24 VCFs (chrom 1-Y) and I want to concat them all into one VCF. But ... for 16 VCFs I have 100 samples and for the remaining I have 95. The 95 samples are present in the 100 sample VCF. So is there an easy way to concat (not merge) these VCFs into one? ...
vcf concat bcftools written 3 months ago by QVINTVS_FABIVS_MAXIMVS2.2k • updated 7 weeks ago by Juan Manuel Berros80
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SNP + INDEL Merging Guidelines
... Say I have SNP INDEL calls for 1000 individuals. These 1000 samples were joint-called and recalibrated with GATK in 10 batches. As a result I have 10 VCF files with SNP and INDEL calls that I would like to merge. I only have access to the VCF files, so re-calling from the BAMs is not an option. ...
vcf indel snp merging written 8 months ago by QVINTVS_FABIVS_MAXIMVS2.2k
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Comment: C: When should you left-align INDELs (and why?)
... Thanks for the clear answer. Do you recommend `vt` or `bcftools` for normalization? ...
written 8 months ago by QVINTVS_FABIVS_MAXIMVS2.2k

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