User: naseerkhan861

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Posts by naseerkhan861

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Comment: C: Deferentially Expressed Genes using Genes count data obtained from RNASeq
... Thanks Benn for your reply, I am reading limma, Thank you very much indeed! ...
written 3 months ago by naseerkhan8610
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Deferentially Expressed Genes using Genes count data obtained from RNASeq
... I have obtained Genes Count data after the analysis of RNASeq dataset , Now I want to analyze my dataset and extract DEGs(Differentially Expressed Genes) as my end goal is to perform clustering using WGCA once I have the DEGs from my dataset, Can somebody guide me how to proceed or guide me any link ...
degs genescount rna-seq written 3 months ago by naseerkhan8610 • updated 3 months ago by Benn7.9k
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How to calculate TIN score of the GSE dataset to perform some post quality checks on RNASeq dataset
... I am working on the [GSE 102741][1] dataset, I have both Raw Gene Count data and log2RPKM dataset , I want to assess the quality of the dataset using PCA analysis by following [Paper][2], How can I calculate the TIN score ? Are there some online tools? can somebody guide me how can we assess the qua ...
quality rna-seq written 3 months ago by naseerkhan8610 • updated 3 months ago by i.sudbery6.9k
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Comment: C: salmon was only able to assign 0 fragments to transcripts
... Thanks as you are always very helpful. ...
written 3 months ago by naseerkhan8610
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Comment: C: salmon was only able to assign 0 fragments to transcripts
... Thank you very much Indeed! ...
written 3 months ago by naseerkhan8610
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Comment: C: salmon was only able to assign 0 fragments to transcripts
... you mean I need to delete whole post and then post it again? ...
written 3 months ago by naseerkhan8610
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Comment: A: salmon was only able to assign 0 fragments to transcripts
... I will check WSL and will run all those commands there, but you can see, I was not having any issues related to downloading or installation or running of some package ...
written 3 months ago by naseerkhan8610
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salmon was only able to assign 0 fragments to transcripts
... I am following [This tutorial][1] to test the working of salmon on my RNASeq dataset. I am using the RNA-Seq dataset from [SRA][2], for testing I am just using the first run that is "SRR5938419"(about 4.85 GB), so after downloading this file , I used [SRAToolkit][3] and using the following ommand, i ...
windows10 salmon docker rna-seq written 3 months ago by naseerkhan8610 • updated 3 months ago by yztxwd290
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Comment: C: How can I select highly variable genes from the RNASeq gene dataset?
... See the great and well explained answer from the person below. ...
written 3 months ago by naseerkhan8610
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Comment: C: How can I select highly variable genes from the RNASeq gene dataset?
... My objective is to do coexpression analysis after I filter some genes with low variance, is that now more clearer to you now what I want to do? ...
written 3 months ago by naseerkhan8610

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