User: kintany

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kintany10
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5 months ago
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2 years, 9 months ago
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Posts by kintany

<prev • 6 results • page 1 of 1 • next >
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Comment: C: CG content changed after trimming the adaptors
... Thank you. I changed the format to pdf, you should the files now. ...
written 5 months ago by kintany10
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CG content changed after trimming the adaptors
... Hi all, I'm analyzing RNA-seq data, paired-end, coming from Nextera. I ran Fastqc to look at the quality and got the following report: [here][1]. So I was concerned with the amount of Nextera transposase left, so I ran trim_galore to trim it. But after trimming the report looks like this: [here][2]. ...
rna-seq fastqc written 5 months ago by kintany10
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Comment: C: STAR output processing
... yes, that's what I'm saying ...
written 2.4 years ago by kintany10
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Comment: C: STAR output processing
... Yes, I'm mapping to two separate genomes. Then I want to use ASEReadCounter from GATK for ASE statistics. It requires BAM file as input so I need to find a way to create this file from two BAM files that I have now ...
written 2.4 years ago by kintany10
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STAR 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 files. I want to keep reads aligned uniquely to only one genome and in cases where reads mapped uniquel ...
ase star rna-seq written 2.4 years ago by kintany10
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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 estimate dispersion for each gene ("dispGeneEst" in DESeq2) that represents variability of expression ...
rna-seq written 2.8 years ago by kintany10

Latest awards to kintany

Popular Question 20 months ago, created a question with more than 1,000 views. For STAR output processing
Popular Question 20 months ago, created a question with more than 1,000 views. For Expression variability between 2 groups of genes

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