User: grant.hovhannisyan

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Posts by grant.hovhannisyan

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Comment: C: STAR for bacterial genome
... Thanks, very helpful. Are you aware of any comparison (paper or post) between STAR and lets say bowtie2 or bwa in case of bacterial data? ...
written 21 days ago by grant.hovhannisyan270
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STAR for bacterial genome
... Hi Biostars, Is it fine to use STAR for bacterial data (no splicing)? Any comments/suggestions are highly appreciated. Thanks ...
star prokaryots written 21 days ago by grant.hovhannisyan270 • updated 21 days ago by Nicolas Rosewick5.7k
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Comment: C: Read count correlation between samples
... Also depends on whether your samples are technical (usually higher correlation) or biological replicates. ...
written 24 days ago by grant.hovhannisyan270
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problems with updating deseq2
... Hi All, Previously I was using the old version of DESeq2 and now decided to update to the latest one. I have updated R and Rstudio. When I do source("https://bioconductor.org/biocLite.R") biocLite() I get Bioconductor version 3.5 (BiocInstaller 1.26.1), ?biocLite for help ...
R deseq2 rstudio written 28 days ago by grant.hovhannisyan270
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Comment: C: DESeq2 with subset of genes
... Parental-> mapped to parental genome -> 90% unique maps Hybrid-> mapped to phased genome -> 2.5 % unique maps Parent-> mapped to subset (300 genes) -> 2.9 % So I think I will subset these 300 genes from the whole genome mapping, and will normalize the library size only ...
written 4 weeks ago by grant.hovhannisyan270
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Comment: C: DESeq2 with subset of genes
... 2% to 300 genes (the rest are multimaps), and 90 refers to entire genome. I used used STAR-DESeq2 pipeline. What I want to try is mapping the parent only to subset of these 300 genes and then use DESeq2. ...
written 4 weeks ago by grant.hovhannisyan270
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Comment: C: DESeq2 with subset of genes
... Hi Devon, allele-specific expression is exactly what I had to do, that's why I phased genes :) So now I want to compare the parent and homeolog. Here we have a quite complex genome and usual allele-specific pipelines fail, since >70% of genome has undergone conversion and LOH. ...
written 4 weeks ago by grant.hovhannisyan270
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Comment: C: DESeq2 with subset of genes
... Hi Venu, you right, my gut feeling says that conceptually it might not feet to DESeq2. Regarding ANOVA, what do you suggest exactly? Thanks ...
written 4 weeks ago by grant.hovhannisyan270
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DESeq2 with subset of genes
... Dear All, I have RNAseq data of a hybrid yeast, which has a lot of gene conversion and loss of heterozygosity between two genomes. I also have RNAseq data of one of its parents. I was able to phase only 300 genes out of 6000. What I want is to compare gene expression levels between hybrid and this ...
hybrid deseq2 rna-seq written 4 weeks ago by grant.hovhannisyan270
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Comment: C: IGV with subset of bam file
... well, I extract them not from the particular region of interest or the region that I know in advance. ...
written 6 weeks ago by grant.hovhannisyan270

Latest awards to grant.hovhannisyan

Supporter 8 weeks ago, voted at least 25 times.
Scholar 12 weeks ago, created an answer that has been accepted. For A: Change sequence in SEQIO
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For C: weird STAR output, bash scripting problem
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: gatk tool installation problem
Scholar 4 months ago, created an answer that has been accepted. For A: Change sequence in SEQIO

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