User: Jay-Run

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Jay-Run10
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Posts by Jay-Run

<prev • 13 results • page 1 of 2 • next >
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Comment: C: Is there a stagewise testing procedure for DESeq2?
... Of course. I'd be more than happy to share my experience with others. Thank you. ...
written 7 weeks ago by Jay-Run10
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Comment: C: Is there a stagewise testing procedure for DESeq2?
... Thank you, Devon. I read this vignette a while ago in which they performed stage-wise limma-voom and DEXSeq analysis. I'm gonna have another look and see what I'm missing. Happens a lot since I'm at the beginning of the road. Best, ...
written 7 weeks ago by Jay-Run10
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Is there a stagewise testing procedure for DESeq2?
... I'm trying to perform a differential gene expression analysis in which I want to compare edgeR and DESeq2 methods. I've already done the stagewise testing for edgeR and was wondering if there's a stagewise testing procedure for DESeq2, as well? Thank you. ...
R next-gen rna-seq sequencing written 7 weeks ago by Jay-Run10
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Comment: C: High mapping on chromosome M in RNA-seq data
... Thank you very much. I'm just gonna do the DE analysis and see what the results suggest. I will take these into account. Best regards ...
written 7 weeks ago by Jay-Run10
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Comment: C: High mapping on chromosome M in RNA-seq data
... I forgot to mention that I tried read distribution, too, in which about 48% of the reads are mapped to CDS-Exons, and the other half mostly mapped to 3UTR-Exons, and introns. And some to TSS-up-5kb and TSS-up-10kb! So, you don't think this is typical for tumor data? ...
written 8 weeks ago by Jay-Run10
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High mapping on chromosome M in RNA-seq data
... Hello! I'm working with RNA-seq data (tumor tissues sampled from female and male patients). After mapping, only 29-55% of reads are assigned to exons, and 39-60% are unassined-MultiMapped. Is this reasonable for RNA-seq data? I also checked the number of reads mapped to each chromosome. Some of ...
next-gen rna-seq written 8 weeks ago by Jay-Run10
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Comment: C: Is first strand the sense or the antisense?
... Thank you for providing me with a solution. Unfortunately, I cannot work on the server to convert RNA-seq reads to counts, because it's too heavy and I'm afraid it will crush the server. That's why I decided to use Galaxy to get my count matrix and then do the rest of the analysis in R. So, if I c ...
written 8 weeks ago by Jay-Run10
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Comment: C: Is first strand the sense or the antisense?
... The the scan information, SC019_core_rEXT009.180913.HiSeq4000.FCB.lane4.gcap_17_11.R1, implies R1 and the the column library strand is first strand. In the stranded library prep, the first strand which is made based on the original mRNA is kept and the second strand is digested. Thank you. I will ...
written 8 weeks ago by Jay-Run10
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"No samples found with any adapter contamination > 0.1%" Is adapter-trimming still necessary?
... Hello, everyone, After running fastqc on my raw data, I realized that the adapters are already removed (>%0.1). Would adapter-trimming in this case still improve the sequence quality? Or I can just skip it and only apply the quality-trimming? Thank you. :) ...
next-gen rna-seq written 8 weeks ago by Jay-Run10 • updated 8 weeks ago by GenoMax94k
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Comment: C: Is first strand the sense or the antisense?
... Thank you, Albert. I know what you mean, and the thing is I totally understand how the stranded or non-stranded libraries are generated, still a bit confused when I want to define the parameters for my analysis. In the multiQC of Infer Experiment, it's clear that when approximately equal numbers o ...
written 8 weeks ago by Jay-Run10

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