User: garbuzov

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garbuzov20
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Posts by garbuzov

<prev • 6 results • page 1 of 1 • next >
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Incorporating factors of unwanted variation from RUVr into EdgeR cell means model for DE
... Hi there, I'm new to working with EdgeR's generalized linear models, but I have a data set where I'm trying to get complex comparisons between groups, times, and treatments, so here I am... I've figured out that the best approach for me is to use the cell means model. Right now I have three time ...
R ruvseq ruv glm edger written 11 months ago by garbuzov20
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Answer: A: 44% Successfully Assigned Fragments with featureCounts after 85% uniquely mapped
... Ok, I think I understand what you're saying. I was so busy comparing percentages I didn't look at read counts. So, for STAR I get: Number of input reads | 73019489 UNIQUE READS: Uniquely mapped reads number | 6236058 ...
written 11 months ago by garbuzov20
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44% Successfully Assigned Fragments with featureCounts after 85% uniquely mapped reads with STAR
... Hi there, I'm wondering if anybody can shed some light into what is happening during the count table step with featureCounts. I am loosing more than half of my reads. My mapping statistics seem to be fine when I run STAR. My library is 75bp paired end using the Nugen Ovation Universal kit. The RN ...
alignment featurecounts star rna-seq written 11 months ago by garbuzov20
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Multi-mapping High with featureCounts but not STAR
... Hi everyone, I am sequencing neurons isolated from rat. I'm working with a limited amount of material, so using Nugen Ovation Universal library kits. The QC using FastQC looks ok. My library is paired-end with 75bp reads. I ran STAR using this command: STAR --runThreadN 3 \ --genomeDir .. ...
alignment rna-seq sequencing written 11 months ago by garbuzov20
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Comment: C: Using SRA Toolkit and Samtools to look at reads mapping to one region in public
... So, to clarify, you are saying the SRA file I am working with is not aligned so I have to do the alignment myself. I have to download the entire SRA file (That's what I'm trying to avoid.) From looking at the GEO how can I tell if the SRA is aligned? ...
written 2.6 years ago by garbuzov20
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Using SRA Toolkit and Samtools to look at reads mapping to one region in public database
... Hi everyone, I'm new to querying public data, so bear with me. I am interested in chip-seq reads mapping to a specific region of the genome and I want to quickly query lots of different data sets for this region. From googling around this is the method I came up with. I tried it first on a positi ...
sra alignment chip-seq written 2.6 years ago by garbuzov20

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