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Forum: RNA Sequencing 02-19-2017, 06:41 AM
Replies: 0
Views: 2,376
Posted By kintany
STAR BAM output processing

Hi all,

I'm running STAR to align RNA-seq reads separately to paternal and maternal genomes for subsequent analysis of allele-specific expression with GATK tools. So as an output I have two BAM...
Forum: Bioinformatics 12-09-2016, 01:12 PM
Replies: 3
Views: 1,612
Posted By kintany
Brian, thank you for the answer! Reference...

Brian, thank you for the answer!

Reference bias is generally not about sensitivity. It is allelic mapping bias: read carrying the alternative allele of a variant has at least one mismatch, and...
Forum: Bioinformatics 12-09-2016, 08:49 AM
Replies: 3
Views: 1,612
Posted By kintany
Arrow Allelic Imbalance with GSNAP

Hi,

I'm working on creating simple pipeline for allelic imbalance analysis for our lab. We want to analyze allelic imbalance for F1 crosses between two mice strains (CAST-EiJ and 129S1-SvlmJ). So...
Forum: Bioinformatics 11-02-2016, 08:01 AM
Replies: 2
Views: 1,617
Posted By kintany
I do the analysis for dispersions of counts, not...

I do the analysis for dispersions of counts, not counts themselves. Length is not correlated with dispersion and has the same distribution for both groups. The same about GC content
Forum: Bioinformatics 10-18-2016, 08:12 AM
Replies: 2
Views: 1,617
Posted By kintany
Expression variability between 2 groups of genes

Hi, I'm analyzing GTEx data (read counts, ~30 patients, one tissue) to check if expression variability is different for 2 groups of genes (I'm interested in one special set on genes). With DESeq2 I...
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